A boy meets a girl of his dreams, falls in love with her, is reciprocated, and all seems shiny... until The Reveal that the girl isn't quite compatible with him biologically. For example, she is an alien. Or a ghost. Or a demon. Or a six-foot praying mantis in a person-suit. Or... Either way, she is not human and that's a slight hindrance in their relationship. How exactly it plays out depends largely on the author:
Fruits Basket: Girl meets boy(s) who turn to have a secret, magical association with the signs of the Chinese Zodiac, and turn into total animals whenever they're hugged by a member of the opposite sex.
Mermaid Melody Pichi Pichi Pitch has an inversion (mermaid meets boy), which is later subverted as the boy isn't entirely human either; they are allowed to remain together. The other members of the Power Trio, also mermaids, get human love interests as well; the manga makes it more clear that they'll probably end up Starcrossed Lovers because of this, but the anime ends on a happier note. Finally, the series' backstory includes other stories of boy-meets-mermaid played straight; one is a legend with an ambiguous ending, but the other... didn'tendwell.
From Vampire Knight, we have Yuki, a human, falling in love with the vampire Kaname. But then we find out that Yuki is actually a vampire as well. All the students at the Night School are secretly vampires.
Space Pirate Mito relates the story of her own reveal to her beloved Kagero to her Half-Human Hybrid son Aoi and asserts that he is the living embodiment of The Power of Love because Kagero married her anyway. Aoi later gets a reveal of his own when the girl he's fallen for turns out to be a Human Alien Galactic Patrol officer staking him out to capture his mother.
Splash: A variation on the classic mermaid-falls-in-love-with-a-human story; she can appear fully human unless she gets wet, which comes as quite a surprise to him the first time it happens.
Let the Right One In. A dark puppy-love version. A Boy meets a mysterious girl and makes friends with her, only to discover, later, that she's a vampire responsible for a series of local murders. Also, "she" is actually a castrated boy.
The 2010 remake Let Me In has the same. Without the twist of the original.
The Deaths of Ian Stone has a peculiar relationship to this trope. In the very beginning, everyone in the setting seems clearly human or clearly inhuman. The second iteration of the main character's Dream Within a Dream reveals that his secondary love interest is both completely inhuman and willing to kill him if he finds out about it. A later iteration reveals that he's inhuman too, albeit with Laser-Guided Amnesia. Unlike most examples, this isn't about the human primary love interest learning to accept him—rather, he learns to think and feel like a human.
The Man Who Fell to Earth gender flips and deconstructs this with alien Thomas Jerome Newton and his Earthly mistress Mary-Lou. They actually consummate their relationship before he reveals his true, Rubber Forehead Alien form to her. Once he does, their already-troubled relationship is only further damaged — out of his disguise, he's not capable of lovemaking in the human manner, and she finds him physically hideous anyway. They ultimately fall out of love with each other.
Played with in Shrek: Princess Fiona finds out that the knight who saved her, the title character, is an ogre. Fiona is taken aback, but continues to travel with him anyway. One reason is because, before they got to know each other, he was only planning to take her to Lord Farquaad, rather than for himself. The other reason is the fact that she's cursed to turn into an ogre herself by night.
Older Than Print: Kitsune are subject to this trope. Kitsune-wives usually left when their true nature was exposed, but in at least one tale, the husband called after her, reassuring her of welcome, so she returned, but only at night.
The Selkie myths of Ireland, almost exactly the same as the kitsune-wives, but the men capture the women by hiding the pelts that let them turn back into seals.
The Huldra women of Norwegian folklore become mortal and gain souls when they are married to a man. However, they still keep their magic and freakish strength, much to the peril of unfaithful husbands.
Subverted in an Arab folktale. A daughter of a ghoul (human-eating monster) winds up with some of its magical powers. She nearly gets married to a prince except for the presence of another girl. She throws herself into an oven and reforms, leaving fresh bread ready in the oven to start a welcoming feast for the prince. The other girl claims similar abilities, throws herself into the oven, and burns to death.
The medieval story of Melusine, which dates back at least to the 12th century, tells of a knight marrying a woman called Melusine:
One version is she marries him on condition that he never look at her naked. One day his curiosity got the better of him and he peeked while she was taking a bath. To his horror he saw that she had a snake-like tail, showing she was a water-sprite or mermaid. When she realized that her secret was out, she left through the window, never to be seen again. In the most common version of the story, this Melusine is the supposed ancestress of the French Lusignan family.
Another version had the condition that she be allowed to be alone, locking herself in her room, every Saturday or Sunday till noon, and the knight would never try to look at or visit her then. This was because she was cursed -by her mother!- to turn into a serpent from the waist down during that time, and did not wish him to know. All of her children were born with some slight deformity, but were otherwise brave, good, and fortunate. But the whispers that the children were deformed because they were not his became too much for the knight, and he spied on her. When she found out, she left him, never to be seen again.
In Greek mythology there were a few examples of this type. For instance, male gods would occasionally reveal who they were on taking leave from the woman they had just impregnated. In a more spectacular example, Hera posed as an old woman to trick Semele, one of her husband Zeus' lovers, into getting him to promise to do her a favour and then make that favour to show himself to her in his true form. She did not survive the experience.
Let the Right One In: as with the movie, a young boy meets a strange girl, and an innocent childhood romance develops, before he discovers that she's a bloodthirsty vampire. The book is even more explicit than the movie about the fact that Eli is a mutilated boy.
"The Girl With the Hungry Eyes": she's a psychic vampire.
"Death on a Barge": she's a regular vampire.
Isabel in Roswell married Jesse Ramirez, who was human, but he didn't find out Isabel was an alien until later in season 3.
Big Wolf on Campus in the second season has this. Human girl Lori Baxter dates werewolf Tommy Dawkins. However, towards the end of the season, they break up because their relationship was getting in the way of their monster fighting.
The main character of Moonlight was turned into a vampire by his wife on their wedding night, who forgot to run it by him first before doing so.
Being Human has werewolf George fall in love with regular human Nina.
In Season 2, ghost Annie goes on a date with human Saul Except he's not so normal himself..., and seemed to have feeling towards normal human Hugh. Also vampire Mitchell is falling for regular human Lucy.
Star Trek 'verse: Boy meets android, or hologram, or Leanansidhe IN SPACE, or astral projection of someone else's subconscious self, or dead Redshirt with instincts of aliens who resurrected her, or long dead to stay and the messages to each other are going through a time warp, or woman whose presence will erase bits of your memory relating to her once she's out of sight... the list goes on. The girls' dating lives are no easier, just not featured quite as often.
Subverted with Tara, who thinks she's a demon and goes to considerable length to prevent Willow from finding out. Turns out she's not; it was just part of her abusive family's "spin to keep the ladies in line".
Xander has been referred to as a "demon magnet", as a good deal of the girls he falls for turn out to be not so human. In "Teacher's Pet" he has crush on a substitute teacher, who is actually a giant praying mantis that wants to mate and then eat his head. He later falls for "Inca Mummy Girl", and in season seven he goes on a date with a nice girl who changes her eye colour and offers him as a sacrifice to open the Hellmouth.
Buffy discovers that Angel is a vampire.
Willow's relationship with Oz is blooming, and then she discovers he is a werewolf. (Though he only found out less than a day before she did.)
Played with extensively in Season 4: Riley discovers Buffy is the slayer (which means demon infused) as she discovers he is a superagent (which is ultimately revealed to be a little bionic).
Charmed: Mid-way through series 1 it's revealed that Piper's (then) boyfriend Leo is not human and that he's a whitelighter. There had been a few comedic suspicions about him prior to the reveal due to Piper's bad luck with men (her boyfriends often ended up being revealed as evil warlocks) but the reveal that he's their guardian angel does come as a shock to all of them. Since whitelighter/witch romances are traditionally forbidden, the couple do spend most of the entire eight seasons struggling to make it work before everything finally works out in the end. Subverted in that whitelighters are actually born human but are transformed into whitelighters and can be turned back into humans if the occasion demands. All three of their children are half-whitelighter, half-witch.
On The Vampire Diaries, Elena unexpectedly meets Stefan and feels an instant connection with him in season one. However, Stefan is hiding a deep, dark secret: he is a century old vampire. As Stefan and Elena fall harder for each other, Elena eventually discovers that Stefan is a vampire.
There was a subplot in the Game Boy Advance RPG Robopon 2 based around this. You have to round up a group of alien schoolgirls on a field trip from the moon (It Makes Sense in Context) and one of them disguises herself as a human and has a guy fall in love with her. You chase them all over the world map. When she finally admits to him that she's an alien, he says that he'll love her no matter what.
This is one of the possible endings in the Interactive Fiction game Afflicted, where you are a restaurant inspector who stumbles across a feud between vampires. After the player reassembles Sofia's body, he can agree to be turned into a vampire himself; if you simply leave Nikolai's Bar afterwards, Sofia ends up moving in with you.
Disgaea 2: Cursed Memories: Boy meets demon. Turns out to be a non-issue since Disgaea: Hour of Darkness already showed that human/demon Half Human Hybrids are possible (and for those who haven't played it, a character from that game explains it anyhow). And it doesn't matter anyway, as boy is a demon too but doesn't realize it. Of course, by that point, it's stopped being "boy meets demon" and started being "boy meets reincarnated God Of All Overlords."
Teddie's crush on Labrys in Persona 4 Arena inverts this. He meets her thinking she was a normal human girl, feeling ashamed of his own non human nature when it is revealed to her soon after. The eventual reveal that she isn't human either, but an amnesiac battle android only makes him more enthusiastic about winning her for himself, if anything.
xkcd has this comic, where the reveal shows unexpected dangers of online dating.
The comic Orange Marmalade focuses heavily on the main character Ma-ri's dilemma to both keep the fact she is a vampire hidden from her boyfriend but also struggling over whether or not she should tell him she is. When he eventually discovers the truth from a third party, he is disgusted and horrified to say the least.
The Monster Girl Encyclopedia: Varies. Several monster girls can disguise themselves really well. Among those, there are some monsters whose will just have fun with male humans, other will seek romantic relationship with their husbands though.
Parodied by a Show Within a Show soap opera in Johnny Bravo, wherein a woman confesses to her lover that she is not what she appears, revealing herself to be a giant dalmatian. In another episode, Johnny goes on a date with a deer. No, not a humanoid deer, part-deer human, anything like that - an actual, albeit talking, deer. In another episode, Johnny goes on a date with a woman who turns out to be a werewolf, and he's actually desperate enough to try to make it work, until he discovers she's hiding an even worse secret.
One episode plays with this trope, in that Johnny goes out on a date with a vampire woman who the audience knows from the start isn't human, but he remains blissfully unaware until the episode's end. She ends up going back to her old (vampire) boyfriend at that point, and Johnny handles the vampire thing pretty well.