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A female character who resembles a pretty, androgynous boy, but in a positive way, usually coupled with an appropriate 'masculine' outfit. Swooned over by confused females as much as outright Schoolgirl Lesbians. Sometimes in the episode they're introduced, they're confused for men until the other characters recognize and treat them as girls. Occasionally, it's also a roundabout way of adding a stereotypically 'male' role to a show that doesn't have (or want) one. Very often subject to at least one Stupid Sexy Flanders gag, sometimes even after The Reveal of their true biological sex.
Interestingly, most versions are Prince Charming types and overwhelmingly 'good' characters. Bifauxnen are, from an artistic standpoint, everything that is positive about masculinity while also not losing anything fundamentally 'woman'. Many characters, in fact, simply heavily associate with traits typically praised in men; the appearance is just another path to that. Most of the time the Bifauxnen is not a Butch Lesbian, and is mostly oblivious to reactions they incite.
The major distinction between them and Tomboys is a direct association with elegance and style, and they often appear older than they really are. Tomboys are often associated with playfulness and immaturity, but are still clearly female. While it is common to have both types of characters in a series, two bifauxnen are less common, and tend to become playful or sexy rivals.
Bifauxnen, however, do not include trans men, as the latter are men, and not simply 'mistaken' for men. Usually they can be distinguished by how they identify, such as Takatsuki from Wandering Son.
This is mainly a Japanese trope. Western examples do exist, dressing this way either throughout a work or in a single scene, but the Western example is generally not straight. Rather, dressing a female character up as a Sharp-Dressed Man was, in European and North American works in the nineteenth and twentieth centuries, a standard Getting Crap Past the Radar way to imply that she was lesbian or bisexual when open acknowledgement and depiction of her sexuality, even in a negative way, would have been forbidden by taste-and-decency standards.
A subtrope of Lady Looks Like a Dude. The male equivalent is Bishōnen. Not to be confused with Sweet Polly Oliver, who only dresses like a man to achieve a goal that requires her to seem male. Compare to Samus is a Girl, where the gender simply isn't discernible until The Reveal. Can also be a case of Bifauxnen and Lad-ette if there's more than one in a particular work or Everybody Wants the Hermaphrodite if she just happens to have a few male bits in the end. Also see The Lad-ette and Attractive Bent-Gender. May involve a Gender Reveal.
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Anime and Manga
Pictured above: Oscar from Rose of Versailles is the archetypal example, more or less cribbed from the otokoyaku (boytype) role of the real-life Takarazuka Revue performers. The Rose of Versailles just happens to be one of their most famous performances.
Kurau from Kurau Phantom Memory. She's very mannish and wears masculine clothing most of the time, the only thing usually giving her away is her voice. Of course, when she pretends to be a man to bodyguard a guy at his wedding, she disguises her voice perfectly.
Masumi Sera's gender is consistently mistaken; the reader isn't even corrected for several chapters. In fact, she is first confused for a molester, and assumed by everyone to be male for the rest of the case. The truth is only revealed when she appears in school the next day - wearing a female school uniform. In a later chapter, Kid Kaitouties her upand steals her clothes in order to disguise himself. He's shocked when Conan informs him that the person he mugged and replaced is actually a girl.
The Sailor Starlights from the final arc also qualify under this trope, at least in the manga, where they're only disguised as boys and not transformed into boys like in the 90s anime.
Ranma ˝: Ukyou, specially around the time of her introduction. From the moment she puts aside her grudge with Ranma and Genma, she switches to a simple Bokukko. (Though she still invokes the looks when at school, as she wears a boy's uniform save for a filler anime where she tries a more open Girliness Upgrade.)
Utena's status is made a bit more complex by her dislike of actually being identified as masculine. Rather, she assumes the qualities of a prince as a heroic, energetic, and proactive figure, and the rest is window dressing; she is clearly a girl wearing a modified boy's uniform and explains her odd red shorts are a concession to playing sports.
Meanwhile, in The Movie retelling, no real reason is given for Utena's 'new' uniform (an unmodified boy's dress uniform) besides the fact it allows one of the major characters to not realize Utena is female until he's halfway into a fight scene. Considering she is also not oblivious to Anthy and Wakaba's flirting this time around, she's a more typical Bifauxnen in this portrayal.
In Kare Kano, Maho Izawa is cast in a play as an android bishounen.
Hana-Kimi: Originally a pretty girl, Mizuki made a good Bifauxnen when she cross-dressed to go to an all-boy school. There, she is revered as a pretty boy. However, when she went back home for the holidays, her father mistook her for a boy upon seeing her with her short boyish hairstyle (not to mention, she was pretty flat too).
Kinos Journey plays with this deliberately, as the title character's gender isn't made explicit to the audience for a couple of episodes. Kino seems to be designed as an "everyman" (well, a woman) who everyone can identify with to some extent.
Maria-sama ga Miteru: Rei Hasekura is a subversion. She happens to be a Kendo Team Captain, tall, and short-haired, but this is the extent of her boyish qualities; her short, delicate-lookingpetite soeur Yoshino is the actual tomboy of the pair. Rei also tends to wear male (or at least male type) clothes when out of uniform, though this could be due to having difficulty find clothes in her size.
Megumi from Tenshi Na Konamaiki is an unusual subversion as she was turned into a girl, and despite being unusually skilled at grooming herself, is mistaken for a one for her rough speech.
Sir Integra. Back when most people's exposure to Hellsing came through the TV series, some people were genuinely confused as to her gender, despite a flashback episode in which, as a young girl, she is clearly shown wearing female clothing. The manga and OVA actually begin with this flashback, making such confusion nigh on impossible.
Rina from Mermaid Melody Pichi Pichi Pitch is more tall and pretty than anything, but she wears the male uniform, and upon her introduction in the anime, Lucia and Hanon wonder, "That was a girl... right?"
Shiratori, Kisara's servant from Kenichi: The Mightiest Disciple. In her first appearance and in every appearance since, she's had a bishonen-esque face and always wore a heavy coat and shirt, showing no hint of her gender. In chapter 489, we get this, revealing Shiratori's real gender for the first time, Takeda's reactions pretty much showing what the readers had thought this whole time.
Minami-ke: Touma Minami (no relation) is first persuaded to pose as a brother, then later insists on being called a boy, even though she's not, probably because all three of her elder siblings are Aloof Big Brothers (to varying degrees). This provides some nice contrast to Wholesome Crossdresser "Mako-chan".
During the Battle Frontier, Ash met Anabel/Reira. Her clothes, short haircut, and ambiguous voice, at least in Japan (and the Latin American dub, by extension), led him to assume she was a guy at first. Not even Brock, who successfully blew up Duplica's similar stunt in the first season, could identify Anabel as female when he met her. The dub screwed the effect up by giving Anabel the voice of a grown woman.
Anabel's even more bifauxnen in one of the manga, to the point where people thought she got a gender change due to the clothes◊ she wore for half of the manga.
The tomboyish Nozomi/Zoey also counts. For added effect, she always wears suits in when competing in contests.
Shion/Cher from an episode of the Best Wishes series. Her masculine traits led some fans question if the castle where she lives actually only accepts women inside, her being mistaken for a man at first.
In the Pokemon Special manga, Yellow is thought to be a boy by the rest of the main cast, right up until her hat gets blown off so they can see her ponytail. Red still thinks she's a guy... for about a year... causing some awkward tension with Misty...and setting up for the best reaction in the entire manga when she finally takes the hat off in front of him.
Miura of Yotsuba&! talks and dresses very much like a boy, so much so that Gentle Giant Jumbo gets confused over her gender when he first sees her.
Rin Asougi from Mnemosyne seems to have this down pat - if it wasn't for her rather large breasts, she could quite often be mistaken for a effeminate man. This is in large part due to her choice of clothes - a man's business suit. It doesn't help that she is by far extremely Badass.
The Wallflower has Sunako-chan turning up at a 'boy/girl mixer' with her classmates, dressed as an extremely pretty boy, because it precludes the chance of any boys asking her out but still fulfills her promise to go out with them. She's,er... special. No, not that way.
Protagonist Ryougi Shiki of Kara no Kyoukai is a subtle example, as there are few extraneous characters to comment on her handsomeness. In the first chapter, every phrase concerning her was written so that her actual gender was not mentioned until the second-to-last line. This probably has to do with her (originally) having two personalities, one male and one female. Though by episode 4 (chronologically 2) SHIKI (the male personality) sacrifices himself in the Void for Shiki (the female personality) to live on, wakes up from her coma, and gaining the Mystic Eyes of Death Perception.
Haruhi mostly doesn't care if she's taken for male or not and often dresses in feminine clothing when she's not at school... but since the rest of the Host Club is determined to keep her gender a secret, she wears a male school uniform. (Not helped by how she actually wore the male uniform before joining the club, since it was cheaper than the girl's one.) And she is considered to fill the "boy so pretty he could be a girl" demographic to the unknowing club customers.
Benio "Benibara" Amakusa of St. Lobelia Girls' Academy's Takarazuka Club, meanwhile, is a fully intentional example.
Yagyu Kyubei is an unusual example - she exemplifies this trope, but not on accident; she was raised as a male. Otae says Kyubei was "born with a woman's body, but a man's heart".
Mutsu is also an example. Doesn't help that she wears men's clothing.
Both Yayoi and Lin from Kure-nai. It's no wonder that they always end up fighting each other.
Kiri from Never Give Up ended up with the looks of her father. Furthermore, to follow her love interest, she gets hired as a male model. Her masculine features are emphasized by her love interest, Tohya, being an effeminate-looking boy. This is often joked about by Kiri's friend, Natsu:
Natsu: I do think you two look good together. Kiri: Huh?! Really?! Natsu: Prince Kiri and Princess Tohya. You'd be best couple in the yearbook, for sure!
In Himegami, there's several bifauxnen hiding almost in plain sight. The protagonist Hyou is one, though the women she protects all know. The primary villain, a French noble named Gawain, very surprisingly turns out to be one after everyone but her servants leave her home, and she undresses to be waited on hand and foot. That suit hides her bust very well.
Ren Radou from Get Backers fits this trope to a T, especially in the manga. In the anime, she's tomboyish but still recognizably female (even without having a voice). In the manga, she's...well, see for yourself◊.
Averted in Angelic Layer, since Sai Jounouchi has the looks but apparently wears a long skirt.
Ice Revolution: Tomboy Masaki is getting tired of constantly being mistaken for a boy (her short Anime Hair, preference for tracksuits, masculine speaking style, aggressive nature, amazing strength and fighting skills, in-denial dojo-owning father and two brothers, one of whom looks just like her don't help), and gets inspired by figure skating after trying to find the only boy who's seen her in a girl's uniform in order to thank him after he saves her from a truck. Unfortunately the coach who discovers her believes he's found the next great male figure skater. It takes another two chapters before that's cleared up and a Wholesome Crossdresser gives her beauty advice.
Kana, the Wrench Wench from Haibane Renmei. She dresses in a boy's uniform and her voice is low enough in tone to be passable for either gender, and every so often someone asks about "him". These aspects of her, however, are only lightly touched upon in the anime.
Baccano!: Ennis is a partial case, being obviously female but prone to dressing and carrying herself like a man in a time period where that didn't often happen. The real Bifauxnen however is Ricard Russo, who's more often taken for a cute little boy than a teenage girl by characters andreaders.
Black Jack: Kisaragi Kei is an early example. She began living entirely as a man after her (cancerous) ovaries and uterus were removed.
Cera Eguchi of Saki Achiga-hen, who has short hair, and doesn't like wearing the Senriyama school uniform, instead going around with a gyakuran top, t-shirt and shorts, thus comes off as looking like a boy.
Kiri-chan from Ga Rei Zero. (Almost a carbon copy of the one in the picture above.)
Shadow in Godannar manages to cross the line all the way to "are you sure she's not a man?" despite having an obviously female body. This is because she manages to be one of the few pilots to contract the Insania Virus, which is supposed to primarily affect men.
After years of doing the opposite in JoJo's Bizarre Adventure, Hirohiko Araki finally revealed Hot Pants' gender in Steel Ball Run. It makes her Stand power, the flesh-spraying Cream Starter surprisingly fitting.
Hetaween 2011 also has Ukraine as one, when she cosplays as the Mad Hatter in the Slavi/Baltic group. Liech dresses up in boyish clothes again, this time cosplaying as the son of Wilhelm Tell while her brother Switzerland is Wilhelm Tell himself.
As well, both Hungary and Belgium wear rather masculine military uniforms. Vietnam's uniform has only been seen in a few sketches, but appears this way as well.
W Juliet: You would never know Miura Ito was a girl unless she told you, especially at the beginning of the manga. Likewise, her boyfriend Makoto makes a gorgeous woman, to the point where all of his male classmates are in denial when they find out the truth at the end of the manga. Ito is constantly given male roles in the school drama club (their teacher is apparently a huge Takarazuka fan), and the one time she was cast as the female lead it was supposed to be a comedy version of Swan Lake, with Makoto as the handsome prince.
Jun of Saki. Short hair, dress shirt and tie, husky voice, usage of male first-person pronouns, and a tall, lean figure? Even some viewers were thrown off by this despite her presence in an all-girl tournament.
Yu-Gi-Oh! GX: Throughout most of the series, Yubel does look female. Actually, she's a hermaphrodite. The confusion sets in when you see her in her formerly human state, where she's a prepubescent girl with a masculine features. Viewers often mistake her for a boy because she was so androgynous.
A character in Monochrome Factor who is employed at Master's bar looks perfectly male as his shirt is always half open and you can see he (she) has a flat chest. However, after he goes a little crazy after telling Maya he (she) is actually a girl and Mayu rejects him, then is possessed by kokuchi she (he) seems to develop rather large breasts...
Nyan Koi!: Nagi is tall and flat-chested, also a gangster (the daughter of a Yakuza family) and the captain of the track team. She used to love girlish clothes and things, but started dressing and acting like a man after her first love rejected her.
Boy Of The Female Wolf features Eun-soo Cha, who passes as a very attractive and hilariously vain ("You dare hurt my beautiful face!?") boy and gets into fights — the difference is she does it 24/7 (going to school as a boy was one incentive to move in with her mom). Her reason is that she sees women as frivolous and weak — her mom effectively abandoned her when she married a guy from overseas; her grandma recovered from a serious illness only to die suddenly, yet another abandonment, and all those schoolgirls fawning over her doesn't help either.
Love In The Mask: The heroine is a bodyguard to a wealthy girl and had to become a boy because "a female bodyguard wouldn't be taken seriously" (despite living with her charge there's no chance of Bodyguard Crush since they're Like Brother and Sister). Apparently it's not too successful since a character who only recently returned to Korea and never met her promptly addresses her with a female honorific and asks if everyone in the entire school is blind.
Akito from Fruits Basket actively fools people into thinking she's a man. Helps that she has a very similar hair cut to Yuki's. Does not apply in the anime where Akito is obviously male. Akito being a Bifauxnen is actually a huge plot point. She was actually forced to act, dress and make everyone believe she was a man, per orders of her horribly abusive mother Ren, who did it out of petty jealousy over how Akito's dad adored her. Out of the Zodiac members, only the eldest ones (Hatori, Ayame, Kureno and Shigure) know that she's a girl and identifies as such despite how she was raised — Kureno later explains this to Tohru in what becomes a MASSIVE Shocking Swerve. The other don't learn this until almost the end, when the now reformed Akito appears in front of them in a female kimono.
Parodied with Yuki, who is quite the case of Dude Looks Like a Lady... and his best friend Manabu tries to trick his girlfriend Komaki into believing he's actually a Bifauxnen.
Kaoru Daichi from Ladies Versus Butlers! is both Akiharu's roommate and a girl crossdressing as a boy. Given what type of series this is, this makes for some awkward tension.
Interestingly, another Itsuki is assumed to be this at first in Haruhi Suzumiya, but the title character quickly decides that "for now, he looked male".
1/2 Prince has a variation. The main character is a girl who takes on the role of a male in a virtual reality MMORPG, very few people see through the disguise, and what few do only manage to do so after she gives herself away.
Ryo Kuromatsu in the manga The Magic Touch. She looks so much like a boy that even when she wears girl clothes, she looks like a guy wearing girl's clothes. Most characters in the manga know she's a girl, though.
Melk the Second from Toriko. Done so she can become the successor of her adopted father, the first Melk, or so she thought. Because he'd already decided she was worthy to be his successor and told her so, except he speaks so quietly she couldn't hear him.
The title character from Musashi Number Nine. The big reveal comes at the end of nearly every issue/story arc, especially early on.
Chizuru from Wandering Son counts at times. She typically looks feminine when in casual wear, but whenever she decides to crossdress in a boy's uniform she does looks like a Bishōnen with long hair. She's gained the attention of a few girls too.
Eureka looks almost like a male in her soccer attire in episode 39 of Eureka Seven thanks to her hair loss.
Jun Kamigamo from Natsu no Arashi! looks unquestionably like a male until the reveal of her true gender.
Halfway through the series Boku wa Tomodachi ga Sukunai, the protagonist Kodaka Hasegawa was surprised to find out that his long forgotten male childhood friend "Sora" was Yozora Mikazuki, who was actually a female.
There's a oneshot manga called Kuroneko Guardian where a young singer is given a bodyguard. She's dressed as a boy because "it'd be easier to work if people didn't know she was a girl".
Elfen Lied: The Agent was confused for a man for almost all of her appearances, but was revealed as female at the very end, where her shirt rips, and reveals her cleavage.
Yuri Ishtar from Anatolia Story/Red River. She was mistaken to be an attractive young boy while she was pretending to be a dancer. She's also mistaken for a boy when one of Kail's brothers comes to visit. Hilarity Ensues.
Played more seriously later, when a local queen is told that "a young boy" is conquering several territories for the Hittites. Said Queen's pre-teen daughter, in a well-intentioned by VERY misguided move, decides to sneak out and offer herself to "serve" said "boy", implicitly in asexual manner, in exchange for the safety of her people. Yuri is shocked at this, then explains the deal to the princess and makes her one of her ladies-in-waiting instead. (Not to mention the girl's mother was not happy either when she found out.)
Lampshaded in Dog Days, where Cinque is surprised that Eclair was a girl.
The plot of I Girl is that a women has to disguise herself as her younger twin brother, who is a high school teacher. He cuts her hair and suddenly looks near identical to her, just with a rounder and shorter face. It turns out that a large number of the students have crushes on her brother...
Kaoru Sayanomiya of Campione! is a powerful miko, head of the Tokyo branch of the History Compilation Committee, and heir to her powerful family. Her only flaw is her tendency to wear men's clothing, even at formal events where she's known to be a woman. Many of her female classmates have fallen in love with her and she makes no effort to correct them on her gender or discourage their attempts to win her over.
Kagerou Days: Kido.◊ During her first (very brief) appearance, Shintaro mistakes her for a guy. She's noted to have a pretty face by other characters, but it (and all aspects of her figure) is usually hidden by her hoodie and hair.
Yuu Kashima from Gekkan Shoujo Nozaki-kun, with her short haircut and preference for men's clothes, is easily mistaken for a pretty guy. She also has a reputation as being the school's Prince, which she takes pride in. It's even used as a plot point in chapter 45, where Wakamatsu mistakes her for being Seo's boyfriend, never having seen Kashima in the school uniform where she wears a skirt.
Kashima at one point parodiee the cliche where boyish girls wish to get a Girliness Upgrade. When she gets a cold her voice deepens, leading another character to wonder if she'll get sad she now seems even more like a boy.. Kashima promptly flaunts her androgyny and masculinity around.
Happened to Jubilee of the X-Men at least once. In a slightly odd turn of events, the dinosaur-riding tribe who made the mistake actually had her half-way to the altar with a choice bride standing by before the misunderstanding could be cleared up.
In the early Star Wars comics, the ones produced by Marvel, there was a prince who went to Luke Skywalker for help; later in the arc it was revealed that this character was that prince's twin sister, as the prince himself had died. In order to keep her planet's morale up, she'd needed to keep his death a secret. At the end of the arc the princess also died, and the two of them met Yoda in the afterlife - the princess was clearly shorter and somewhat narrower-shouldered than her brother, but still fairly androgynous. Without looking at the word balloons, it's actually rather difficult to tell that she's female.
Carrie Kelley, the successor to the Robin mantle in Batman: The Dark Knight Returns, is mistaken for a boy by the police. Somewhat of an inversion on how Robins on New Earth are either mistaken for or portrayed in other media as girls.
Dee from DJINN Way To Home is short-haired and fairly flat (she's only fourteen), so she looks a lot like a boy, albeit a cute one. One of her future teammates teases Will (the woman who plans to adopt her) about her much younger "boyfriend," even when said boyfriend is wearing a Dangerously Short Skirt.
In Victor/Victoria, the title character is played by Julie Andrews. Female both in real life and in the movie, she plays the eponymous Victor, an ostensibly male drag queen. Part of the plot is fueled by various women being very attracted to "Victor" (as a subplot, a few of the male characters have a Stupid Sexy Flanders reaction to "him.")
She played the technically sexless Angel Gabriel for the movie Constantine.
Orlando from the film adaptation of Orlando, who begins as an androgynous man in the 16th century, becomes ageless, and later changes sex into an androgynous woman.
The novel on which the film is based was written by Virginia Woolf, writing it as a fictionalised biography for the author-poet Vita Sackville-West, with whom she had an affair. Vita's son would later describe it as "the longest and most charming love-letter in literature".
Also a feature in many of Tilda's glamour shots. There are several which try to make half of her look like a woman and half of her look like a man. It's strangely attractive.
Conan O'Brien has said that Tilda should play him in a movie. She said she'd do it.
Cate Blanchett playing "Jude Quinn" (Bob Dylan) in I'm Not There. Fetish Fuel ensued. Suffice it to say that Cate makes a rather hot guy. The fact that her voice is very much on the huskier end of the scale helped.
Angelina Jolie in Girl Interrupted was wonderfully Johnny Deppish. She was also androgynous in her role as Legs◊ in Foxfire, and spends the last act of Salt with a short haircut, wearing men's clothes while she's in disguise as a man, complete with facial prosthetics which she removes, while keeping the hair and clothes.
Imogen Stubbs, as Viola/Cesario in the 1996 adaptation of Twelfth Night. Olivia's infatuation is completely understandable...
A short-haired Keira Knightley is mistaken for a boy (and to be making out with the female protagonist) in one scene in Bend It Like Beckham. (*happy sigh*) Although the character is traditionally feminine in some ways, her sportiness, preference for trousers at all times, and lack of interest in enhancing her cleavage create a boyish aura around her (contributing to her mother's suspicions that she's gay).
"All's I'm sayin' is, there's a reason why Sporty Spice is the only one without a fella."
In early drafts she was a lesbian, but the creators then decided that it would encourage the sexist belief that all sporty young women must be Lesbian Jocks.
Laure from Tomboy is androgynous looking. She's able to pass herself off as a boy, and even normally she looks like a boy.. It helps that she's only ten, so a haircut and boys clothes is really all she needs to pass as male.
Some Kind of Wonderful: Watts is just a raggedly dressed tomboy for most of the film, but becomes this in the last act after donning a male chauffeur's outfit.
In Blue Is The Warmest Color, Emma at the second part of the film where she has blonde hair and wears more sophisticated clothing that is expected of a well-respected artist. It also symbolizes the passage of time between the two chapters and how much her character has other priorities aside from her domestic life.
In Anne Rice's The Vampire Lestat the vampirized Gabrielle, Lestat's mom, usually adopts male clothing and hair style to be free to do as she wished. During the time (late 18th century) it was difficult for women to get away with living so independently, so she does this for practical reasons.
Nan Astley and Kitty Butler, of Tipping the Velvet. Both are male impersonators in late Victorian England.
Played with (and subverted) in Diana Gabaldon's Outlander series. Secondary protagonist Bree is a six-foot-plus, strapping Scottish redhead who waltzes around in the 18th century in trousers— but only passes for a man if you're really not looking, and is goggled at, flirted with (with cracks about stepladders) and horrifies her father.
Many female fans were extremely pissed off to discover that Maladict from Monstrous Regiment is, in fact, a girl.
Jame from Chronicles of the Kencyrath is mistaken for a boy on a regular basis, is declared to be officially a boy in a fair few contexts throughout the books, and is mistaken constantly for her twin brother.
Subverted at one point in God Stalk: The courtesan Melissandwho's flirting with her at the timeis entirely aware that Jame is a girl, is amused that Jame thought otherwise, and doesn't particularly care.
Leisl in the Ravenloft novel Vampire of the Mists is a thief who dresses as a boy to survive better on the streets.
In "A Scandal in Bohemia," Irene Adler admits to Sherlock Holmes that she frequently dresses as a man to go out in public because of the freedom that male costume allows her. As shown in theatrical versions of the story, the result is apparently Bishonenesque.
In Mona Lisa Overdrive by William Gibson, Kumiko muses that Molly greatly resembles the stereotype of the Japanese bishonen: "elegant, deadly and fey."
Kitai from Jim Butcher's Codex Alera, partly to do with the fact that she's an underage Marat with vaguely boyish features (until they come of age, Marat wear baggy tunics and aren't acknowledged to actually have any biological sex except in the academic sense). Tavi doesn't much care for her initially, because she was kind of hostile for little apparent reason, but once he realizes she's a girl, he starts to notice she's kind of pretty.
Tzigone, one of the central protagonists of Counselors and Kings, is a very slender and flat-chested young woman, and as she's a Master of Disguise she's quite practiced at tricking people into thinking she's male. She does female disguises too, though.
In the world of A Brother's Price, whores service women. Many of them try to look as much like men as they can, and it's to be noted that men in this world are seen as soft, beautiful, graceful creatures. These wear ivory strap-ons called bones at their groins to complete the look.
In the original pilot for the Get Smart TV show, this was done with Agent 99. When Maxwell Smart first meets Agent 99, she has a pageboy haircut and is dressed in a not-very-flattering chauffeur's outfit. It takes Max most of the episode to realize that she's female.
Actually she comes off quite sexy and clearly female right from the start...but this is Max we're talking about.
Anjali Jay as Djaq in Robin Hood; the most stunningly beautiful "boy" you've ever seen.
The recurring skitcom character, "Pat" from Saturday Night Live was based on this trope. Played by a female actor (Julia Sweeny), nobody (including the audience) ever found out if Pat was male or female.
Ironically, in one of the final episodes of the series Amanda Bearse appeared as an Expy of herself (a classic ladette). It was probably the most obviously female she'd appeared through the entire series.
Franky Fitzgerald from the third generation of Skins, but only in Series 5.
In the Seventh Heaven episode Don't Take My Love Away, the youngest daughter Ruthie wants to wear a tux to her parents' vow renewal ceremony. In the same storyline she doesn't want her brother Simon to move out of their bedroom.
Annie Lennox of Eurythmics deliberately plays up her androgyny. Some American audiences were shocked by the video Love Is a Stranger because they thought that Lennox was a man in drag.
The dancers in the video for "Blame It on the Girls" by Mika are half-Bifauxnen: their costumes and wigs make their right half look like a girl in a dress with a bob, while the left half looks like a man in a tux with Beatles hair. See it here.
It should be noted however that Sheik is always described as a she in the Smash Bros games. Also in those games, while Sheik's standard grunts sound masculine, any time Sheik is severly hurt or stressed (such as being tossed across the field) her screams become more feminine as if to suggest Sheik is making a conscious effort to pretend to be male rather than actually transforming into one.
Bloodline Champions has the Nomad bloodline's Officer outfit. There's has cleavage on her, but otherwise looks very androgynous. There's a piercing under their lip which one could mistake for a soul patch.
King from The King of Fighters. She dressed as a man in the original Art of Fighting, due to an incident regarding her gender and childhood training in Muay Thai (which back then didn't accept female practitioners), as well as being forced to be a bouncer by a local gang. In that game, she is presented as a male at first (besides baring her bra if beaten with a super move and having different dialogues when this happened), but future games acknowledge her as a woman who chooses to wear male clothes both for personal taste and practical reasons. She continues to dress in masculine clothing in almost all her later appearances; the closest concession, clothing-wise, is either wearing dresses in artwork and in her ending in The King of Fighters XI (and the last one is because she is in a date) or showing up in two-piece swimsuits in the Dating Sims.
Razzy, a major supporting character in the underrated gameSummon Night: Swordcraft Story is very ambiguously gendered (To characters anyways, she's first introduced as another character's "niece"). In fact, throughout a good chunk of the game, the player character and various NPCs think that Razzy is a boy. One NPC even comments that Razzy will be a handsome man when he grows up. Coupled with this boyish look is that, out of the five available weapons in the game (sword, axe, spear, knuckles, and drills), Razzy uses knuckles. Also adding confusion is that it is hinted that (read:Immediately starts addressing you as Onee-sama and directly wonders if two girls can get married), while playing as the female option, Pratty, Razzy will acquire a crush on you.
Hikaru of Power Instinct Matrimelee is a almost a parody of characters like Bridget from Guilty Gear (like many characters in the game). Her gender is so well hidden that nothing in the game itself actually mentions it, not even in her ending. The only way someone would be able to determine her true gender is from other documentation.
This◊ is what Amano originally drew her as. The SNES's graphics messed the twist up. (Except for fans who assumed that the pretty, long-haired man was one of the series' many Long Haired Pretty Boys.)
Lightning from Final Fantasy XIII generally doesn't qualify due to her obviously feminine appearance in the game... however, she later pose for a fashion magazine... men's fashion magazine, that is. In the third game in her series, she can wear men's suits, and gets mistaken for a prince in the NPC chatter.
In Persona 4, one of the main characters, Naoto Shirogane, the masculine, pistol-wielding, uniform-wearing, amateur detective-turned high school student is a biological woman dressing as a man because she believes that she won't be taken seriously in a mostly male field of work. After her gender and identification are revealed, Naoto decides to keep the boyish looks and behavior — unless she's specifically asked otherwise by the Protagonist, and only when they are alone.
Izanami's human form looks a lot like the Protagonist, despite being a woman, and looks even more boyish in the manga.
Maria Tachibana and Kanna Kirishima are tall and have husky voices, so they usually play male roles in their musical productions.
Later we get Leni Milchstrasse, who is petite and waifish and talks like a boy.
Subaru Kujou from Sakura Taisen V sits squarely between Bifauxnen and Transsexual territory. She occasionally refers to herself with female pronouns and does not mind when others do the same, but she staunchly refuses to actually identify as female or male, and her gender is questioned at various points throughout the game without a clear answer ever being supplied. The word genderqueer was invented for people like her.
Toyosatomimi no Miko, who's based on a real male historical figure and has a hefty dose of masculine arrogance, though she still wears a long skirt as part of her outfit.
An obligatory PC-98 example, Meira from Story of Eastern Wonderland, whose demands to fight Reimu for her powers were mistaken for a proposal by Reimu... and accepted. Meira clarifying her gender didn't help.
Atelier Annie: Annie is practically the embodiment of this trope. Seriously, look at this and see what your reaction is... If the existing image wasn't so good, she'd be the banner girl for the trope. Of course the game itself wastes no time in poking fun at her for this, with several NPCs mistaking her for a boy at first glance.
In SaGa Frontier, Asellus is a girl who is mistaken for a man by a maid who made a suit for her, who develops a crush on her. According to a sourcebook, this (and Asellus's feelings for her companion, Lady White Rose) is due to the magical blood transfusion she got from the Charm Lord, a Dracula-type character. (It doesn't help that the Lord insisted that Asellus become the "Prince" (not princess) of his kingdom.)
From Infinite Undiscovery: Vic's true gender soon becomes fairly obvious, with several hints shortly after Vic joins your party.
It is possible to make female Shepard this in Mass Effect if you manipulate the face sliders cleverly and choose only the gender neutral clothing options and the three shortest hairstyles. Granted, her chest will always be visible, but Shepard can become quite masculine.
Leo Kliessen from Tekken 6. Short hair, check. Masculine name, check. note Her full name is Eleonora, and "Leo" is a nickname Masculine outfit, big check (includes a white masculine tuxedo).
Halo: The "tough" type female Marines (voiced by Michelle Rodriguez), and Kat in Halo: Reach.
Olga Gurlukovich. She has shorter hair than either male protagonist, wears masculine military clothes, and, at one point, a male character (admittedly, the resident Bishōnen) is mistaken for her. She also pulls off a Samus is a Girl as the Ninja.
The Boss also qualifies, given her harsh features, muscular body, and complete lack of adherence to Stripperiffic clothing (when you first meet her, she is wearing the exact same uniform as Snake, and she was the first person to use the sneaking suit). Arguablyly, having her hair unbound makes her look more masculine than when it is bound back (compare this picture◊ to this one.
Peace Walker has Strangelove, with her short hair and androgynous tailored clothes.
Perfect Dark: Joanna Dark in the original, less so in the XBLA rerelease.
Kumatora from Mother 3. A little kid mistakes her for a boy at one point. And the Magypsies.
Jess from Advance Wars has a buzzcut and wears a military uniform with pants. If not for her name and some *slight* bumps in the chest region, she'd be indistinguishable from a male. The second game enhances this effect my making her carry around a somewhat phallic-looking tank shell.
Ione of Vanguard Bandits is more than a little manly in appearance to the player. This doesn't stop The Hero from complimenting her beauty anyway.
Until her more feminine design in Nuts & Bolts, Kazooie.
Miyako Yakumo from Harukanaru Toki No Naka De 5. She looks completely like a boy, dresses like one, fights like one and has an ambiguous voice to boot.
Makoto Kikuchi from The Idolmaster was raised to be more like a boy by her father, who wanted a son, and thus she looks and acts very masculine out of habit. However, what she really wants is to be more feminine and get more attention from boys, so she became an Idol Singer to reinvent herself. Unfortunately for her, the majority of her fanbase In-Universe is made up of girls with crushes on her.
Yuri from Harvest Moon: A New Beginning would probably be mistaken for a boy a lot more often if she wasn't introduced as Emma's daughter and one of the girls the male player character can marry. (She is also a secret bachelorette, meaning only those who go to sites that show all the potential candidates will know she is one.)
A Female Morgan. It makes sense since, depending on whether the Avatar is a man or a woman, Morgan can be either a guy or a girl. The main physical differences between a girl Morgan and her Distaff Counterpart are her finer features and her sliiiightly longer hair.
Assassin's Creed IV: Black Flag: The character first known as "James Kidd", and actually named "Mary Read" is quite clearly voiced by a woman, and is revealed to be one midway through the game.
They Are My Noble Masters: Averted was Natose, who is a semi-bifauxnen, the only thing is she has boobies (huge ones in fact), and she wears panties under her clothes.
Fate/stay night: Saber aka Arturia Pendragon, having been stopped in her natural growth at around the age of fifteen, can and has posed as a man several times, although a very Bishōnen man. However, it's also implied that she's been under a genuine Gender Bender spell at times in her backstory.
She dresses in more contemporary menswear in Fate/Zero, a sharp, formal black suit. Irisviel fixates on what a handsome protector Saber makes, and contemplates what a beautiful couple they make when she's escorted in public by her. Kiritsugu's partner Maiya also dresses rather austere and masculine, and keeps her hair short.
Rei Ijuin, of Tokimeki Memorial 1, who has to pose as a boy in front of everybody due to a family custom, and this until her coming of age. It's a well-kept secret the Ijuin family zealously protects, to the point that even her little sister Mei doesn't know she's actually a girl!
Asha from Kubera. So much that Ran still thinks she's a guy even though she is wearing a dress. Yes, he thinks of her as some weird guy who dresses up in women's clothing.
Building 12, by Chris Hazelton's: Alex. She was selected to an exclusive program to fill a diversity quota because her application was smudged and they thought she was a guy (it gets mostly female applicants), so now she's pretending to be male.
El Goonish Shive: A weird example, Tedd accidentally sets off his transformation gun and is turned into a girl. His friend doesn't notice until Tedd points out the twins. Then it overlaps into a weird mix of Real Life and Wrong Genre Savvy: he transforms in an off-continuity Q&A-style storyline. The next strip? 'A ridiculous number of viewers claim they didn't notice I was a girl in the last installment until they noticed Grace was a guy!'
Phani: Had she the look of a real woman, she sould have been more lucky in love. Zala: Do not mock her so. It is not her fault if she looks like a man... a very pretty man.
In a few strips in Sinfest, Monique played around with dressing and styling her hair in a very androgynous way to mess with Seymour and have fun with Slick and Squig, but after being exposed to the Patriarchy, she adopted this look as her default appearance.
Dacey Ashcroft of Survival of the Fittest version 3 is described as being very ambiguous in gender - especially since she is very tall for a girl and in general, just doesn't act 'girly'. That she deliberately perpetrates this charade doesn't help matters for the confused.
During one Global Guardians PBEM Universe story, a new hero named The Rook joined the Global Guardians. It took almost a year to figure out that the team's new superhero was actually a new superheroine.
Cybersix: The title character's secret identity involves wearing glasses, recombing her hair and dressing as an English teacher named Adrian, and manages to fool everyone). She dresses in much looser clothes which hide her figure and speaks in a lower voice.
Sonic Sat AM: Sally Acorn is an unintentional example. She is pretty much one of the only female characters in the entire franchise to dress in the same manner as the males.
Female crossplayers are a particular real-life version of this trope, as groups will often pick their most masculine-looking female friends to cosplay Bishounen characters. This will often lead to bizarre situations occurring at Anime conventions, though people have generally learned not to question the gender of those entering bathrooms.
Pop singer/rapper Amber Liu of the Korean girl group f(x), whose androgynous image has resulted in lots of Even the Girls Want Her among the group's female fans. Look at her in this music video. I dare you to think otherwise.
Janelle Monáe, the genre-blurringGenki Girl singer, is rarely seen without her proper tux and a white starched shirt. It also helps her bifauxnen image that she has what can only be described as "epic hair."
Taiwanese singer Zhang Yun Jing, known for her androgynous image. She has been described as both "handsome" and "beautiful". Even the Girls Want Her, as her a large part of her fandom is comprised of females who take great pleasure in squee-ing over her various attractive features, masculine or feminine.
In Andrew Loomis's Drawing the Head & Hands, he more or less sums up this trope when he talks about how artists have more leeway in drawing masculine looking women than feminine looking men (keeping in mind this was in the early 20th century, before bishonen characters became popular).