This is something of a logical counterpart to Common Eye Colors: If a character has freaky, cool, or otherwise unusual hair colours, their eyes are liable to match. "Unusual", of course, needs to be taken with a grain of salt when it comes to Anime Hair. Comic books and western animation are also likely to display this trope.
Some series use this to make a character stand out as being "weird" or "different", especially if it's an uncommon color. Others use this for their entire cast.
May be used as a form of Technicolor Eyes.
Not to be confused with the carpet matching the drapes.
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Anime and Manga
Just about every character in the Fruits Basket manga, except the characters with black hair, who have dark gray or dark brown eyes, and the natural blondes, who have brown eyes.
A great deal of the cast of Sailor Moon matches this trope. Of the heroes, Chibiusa, Ami, Michiru, anime Rei, and Hotaru. And in some artbook pictures, all of them do, including Sailor Moon herself. Of the rest of the cast, all of the Witches Five, several of the Anima-Mates, and Princess Kakyuu.
Dijiko (green eyes and hair), Puchiko (brown hair and eyes), and Hikaru (pink hair and eyes) from Di Gi Charat
Lina Inverse of the Slayers fame is a red-eyed redhead, and Xellos is purple-haired with lavender eyes.
Hikaru and Umi from Magic Knight Rayearth have red eyes/red hair and blue eyes/blue hair respectively. Originally, the third of the trio, Fuu, was going to have green hair to go with her green eyes, but the artists decided on giving her blonde hair instead, though some manga art make it a greenish yellow. Interestingly, the "color-coordinated" jokes went to Fuu and her sorta love interest Ferio, who has green hair and yellow eyes.
Bulma and her daughter Bra from Dragon Ball Z. Her son Trunks retains his purple hair.
Daisuke (red hair and eyes), Dark (purple), Satoshi (blue), and Krad (yellow).
The Harada twins both have brown hair and brown eyes. In the anime, this was interesting because Riku's hair was changed to red instead of brown, but her eye color remained the same, implying that she might have dyed her hair in order to look different from her sister.
A lot of characters have this problem. Rima, Ikuto, Ran, Miki, Dia, Yaya, Nikaidou, Kusu Kusu...
It seems most guardian characters are like this, with the exception of Pepe, who has blue eyes, Suu, whose hair is blonde while her eyes and outfit are green, Il, who has red, and El...whose eyes are always closed.
Most characters from Seto no Hanayome have this eyes/hair match. Sun has gold and Luna has pink (but it's opposite for their mermaid tails - Sun has pink and Luna has yellow). Mawari has a violet combination. Shiranui and Class President have light green eyes and hair. Other characters have more natural combinations of hair and eyes (black or brown).
Very common in Baccano!, as demonstrated by Rachel, Nice, Nicholas, Luck, Ronnie (yellow), Claire, Ennis (reddish-brown), Czeslaw, Dallas, Jaccuzi (brown), and Sylvie (gray). Even more so in the books, where color illustrations apply this to Firo, Isaac, Lua, and Eve as well (not to mention the not yet animated characters).
Most of the characters in Hidamari Sketch have matching hair and eye colors. There's the four main characters (brown, yellow, blue, and pink), Yoshinoya (green), the landlady (brown), Chika (light purple), Natsume (blue-green), Nori (blue gray). In fact, the only character who doesn't is the Principal, and that's only because you never see his eyes.
Though Death Note is very good about natural eye and hair colours - all the Japanese characters have brown or black eyes. Misa wears tinted lenses - her eyes change between brown and blue. Light's hair is probably bleached.
The shinigami Watari (golden-blond hair and amber eyes) and the villain Dr. Muraki (silvery-gray eyes and silvery-white hair) in Yami No Matsuei.
Special mention goes to Kyou Kara Maou for making this a plot point. Shibuya Yuuri's looks (including his black/dark brown hair and eyes) are considered average in his native Japan, but when he ends up in a demon country in another world where the combination is extremely rare, he is hailed as a 'soukoku' (double black) and considered highly attractive and regal looking as a result.
Midori from Midori no Hibi, also notable as the only character in the series (besides her mom) to have naturally unnatural hair color.
Lawrence from Spice And Wolf has gray eyes with gray hair - even though he's only 25.
As depicted on the manga covers of Liar Game, Nao Kanzaki and Shinichi Akiyama have (respectively) orange and yellow hair and eyes.
All of the named girls in Puella Magi Madoka Magica; Madoka (pink), Sayaka (blue), Mami (blonde hair and gold eyes), Kyouko (red), Hitomi (green)...except Homura, who has black hair despite being associated with purple (though it's possible that purple is used because black or grey eyes wouldn't look right, and a Soul Gem being gray or black means something else entirely).
The same occurs with the main cast of Vividred Operation. Even the girls' names invoke their colors.
Wandering Son characters are made to fit this lately. As all characters are either brunettes or raven, the characters all have brown or black eyes. Originally, this trope was subverted, as everyone had Brown Eyes. The mangaka makes sure to make the eyes have the same shade as the hair, too.
Ai No Kusabi has Riki with black hair to go with his black eyes, which is significant to the plot.
Ririchiyo (purple), Karuta (pink) and Zange (red) of Inu X Boku SS.
Science Ninja Team Gatchaman has Jun, who has not only green eyes but green hair as well. Averted in the OVA version, however (though they had initially considering making both her hair and eyes blue).
Polaris and Psylocke both have unusual hair colors (Psylocke's is purple, Polaris' green), and their eyes match. The New X-men's Surge has blue hair and eyes.
Of course, Psylocke started out as a blonde who dyed her hair purple, then got (against her will) bionic eyes to match (after losing her original blue eyes), then got body-swapped into a Japanese body and dyed her black hair purple.
Ditto for Surge: when asked, she confessed her blue hair "came from a bottle".
Polaris is all natural, though (when we first met her, her hair was dyed brown. Green is its natural color.)
Melisandre, from A Song of Ice and Fire, has red hair and eyes. She also always dresses in red and worships a god associated with the colour red as well. Averted with just about everyone else, though, with the exception of 'Young Griff', whose eyes are a curious shade of blue to match his dyed blue hair. He's actually Aegon Targaryen (supposedly), and it's a clever disguise, hiding both his distinctive Targaryen hair (silver) and eyes (purple, but reflect the blue from his hair).
"Bess, the landlord's daughter", the love interest of the titular bandit in the poem "The Highwayman", has black hair and black eyes.
Ilse Burnley from L.M. Montgomery's Emily of New Moon has yellow hair and yellow (actually technically very, very light brown—"almost amber") eyes.
Doc Savage has bronze-flecked eyes to match his bronze-flecked hair and skin - hence the "Man of Bronze" moniker.
Deanna Troi has black hair and eyes. The eyes are a Betazoid racial trait.
With only a few exceptions, every Vocaloid has this going on.
Keele Zeibel in Tales Of Eternia is a double example of sorts; his hair colour is either blue or purple depending upon the picture you are looking at (and has varied widely in shade and intensity of said blue or purple, besides...), with his eyes always being blue or purple to match.
Due to hardware limitations, everyone whose pupils aren't completely black/a dark dot in the first three games. There are a few exceptions however.
Ema Skye, who, throughout the games, both averts and plays straight this trope, with her amazing color-changing eyes, which are of a bright blue color in the first game (she has brown hair), but seem to be of a rather brown-ish color in her small profile picture in Apollo Justice and during her appearance in Ace Attorney Investigations.
Most of the main characters are subject to this trope—the only notable exceptions are Rose (black hair/green eyes), Ledah (blond/red eyes), and Malice (blond/blue eyes). And maybe Cierra, whose eyes are reddish purple.
From the same series, we also have Maria and Meria, the heroines of Knights in the Nightmare. Their antagonist counterparts, Marietta and Melissa, are no different.
To make matters worse, a few gym leaders' eye have been recolored to match their hair color. Yes, I'm talking about Whitney◊ and Falkner◊ (and Jasmine◊).
Game Freak has been doing this with most of their characters lately. It's very apparent with the protagonists, where only Brendan◊ and May◊ have different colored hair/eyes.
Wally IS this trope. And not just his hair and eyes, his pants and even his Pokémon (manga-wise) are all green. And in the Adventures manga, he had to wake up Rayquaza. Needless to say, it's green◊.
Generation V seems to have cooled down on this trend because the new female protagonist has brown hair and blue eyes. The male plays this straight though.
The whole party except for Mizuti in the first Baten Kaitos game seems to have this. Kalas with blue hair and eyes, Xelha with blonde hair and yellow eyes, Lyude with red hair and red eyes, and, finally, Savyna with dark purple hair and dark purple eyes. * Touhou
A good number of the girls of Gensokyo have this trait - most notably, Marisa Kirisame with her golden hair and eyes.
In the PC-98 series, pretty much everyone has this, because of 16-bit palette limitations.
Etna from the Disgaea series has red hair and eyes. Though, interestingly, her hair was pink in the first game.
And, by extension, the whole Classic Kirameki Saga, with only two exceptions: Patricia McGrath in Tokimeki Memorial Pocket on GBC (who, as a foreign student, gets the Phenotype Stereotype treatment), and Megumi Juuichiya in the Motto! Tokimeki Memorial Radio Drama stories (who's a rare case of Cute and Psycho in the series).
Kira from Infinite Space has mint-green eyes and hair. In the artbook, the Schneizer brothers' eyes have the same color as their hair (Bastian has dark brown and Dietrich has silver), but in the game, their eye colors are closer to gold.
In Golden Sun Dark Dawn this continues: Rief and his sister Nowell are of the Mercury Clan and have blue eyes and hair, Amiti has blue eyes and hair, one of many hints at his ancestry, and during the final sequences of the game, Matthew's normally blue eyes become gold eyes.
Tali from Mass Effect is a rather more literal example than most, both her visor and hood being purple in color.
Seems to be a characteristic of every character in Sea Princesses, even the ones with blue or pink hair.
All fairies in The Fairly Oddparents have the same eye colour as their hair colour. This is especially noticeable in the episode where Cosmo and Wanda end up taking each other apart with voodoo dolls, then putting themselves back together. One failed attempt had Cosmo and Wanda end up with each other's hair, creating a contrast between Cosmo's green eyes and pink hair, which belonged to Wanda, and vice versa.
Spike as well, for particularly scaly definitions of "curtains".
A few other background ponies get this treatment as well.
In My Little Pony And Friends, there's Buttons (who has blue hair and blue eyes, but has a red streak in her hair as well), Wind Whistler (Pink hair and eyes), Galaxy (her eyes were pink, and her hair was pink, red, and white), Gingerbread (who had blue eyes and blue, purple, and pink hair), Masquerade, Sweet Stuff (Purple eyes with purple, white, and pink hair), Fizzy (Pink eyes with pink, green, and white hair), Rosedust (Pink hair and eyes), Honeysuckles (Pink hair and eyes, though her eyes are blue for the toy), Lily (Purple hair and eyes), Baby Half Note (Turquoise hair and eyes), and Baby Sleepy Pie (Blue hair and eyes).