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Some manga that features a non-binary/x-gender character. Some are headcanons- those are indicated by question marks.

Part 2: https://myanimelist.net/stacks/37987
Part 3: https://myanimelist.net/stacks/55436


Extra non-binary manga that's not on MAL (yet):

Onna no Karada ga Iya nano de Mune wo Torimashita
Kazuki (x-gender) (protagonist)

Then I saw RuPaul's Drag Race': coming out as X-gender in Tokyo
M. A. Joy (x-gender) (protagonist)

Kyouhaku sei Shougai desu!
Asuka Miyazaki (x-gender) (protagonist)

Kyouhaku sei Shougai Chiryou Nikki
Asuka Miyazaki (x-gender) (protagonist)

Unknown Color
Chiaki Hinaga (non-binary) (protagonist)

Quintet×Question
Mokuba Ao (x-gender) (main)

Bloody Chinatown
Kanaya (gender-free) (main)

Bara Shishaku
Gideon (genderless/gender ambiguous?) (main)

Manga that feature transgender boys/men. Some are headcanons- those are indicated by question marks.

Part 2: https://myanimelist.net/stacks/37834


Not on MAL yet:

Akarui
Maki Sanada (trans boy) (protagonist)

Oppai wo Totta Kareshi
Haruka Naruse (trans boy) (main)

Sakura-chan to Amane-kun
Amane (trans boy) (main)

Uchi no Danna ga Kawai sugiru ~tsu! Moto ♀ no Ikemen Nyuuseki Shimashita!!
Husband (trans man) (main)

Chiguhagu
Tooru/Tohru (trans man) (protagonist)

Seishun Minority
Sera (trans boy) (main)

Bokura no VR
Miharu Akina (trans boy) (main)

Ore no Karada wa Nande Onna Nanda?
Ryuutarou "Ryuu" Suzumiya (trans man) (protagonist)

LGBT (gay, lesbian, bisexual, binary transgender, non-binary, genderqueer, intersex, queer, pansexual, asexual, aromantic, etc.) characters in mangas I've read that are not listed as Boy's Love or Girl's Love on MAL. Some are headcanons- those are indicated by question marks.

Anime Version: https://myanimelist.net/stacks/31815

Part 2 (Manga): https://myanimelist.net/stacks/44923


Honorable Mentions for those that are listed as Boy's Love or Girl's Love- even though they really shouldn't be because they're not primarily about MLM or WLW relationships:

Bokura no Hentai
Marika Aoki (trans girl) (protagonist)
Osamu "Parou" Tamura (gender non-conforming and gay) (main)
Ryousuke "Ryou" Kijima (gender non-conforming and bi) (main)
Satoshi "Tomochi" Natsume (gender non-conforming and bi) (supporting)

Kono Koi ni Mirai wa Nai
Yuuji Manase (trans woman) (protagonist)
Kotarou "Tora" Touri (gay) (supporting)
Kaoru (trans woman) (supporting)

Koisuru Sugar Cotton
Chiaki Tabata (trans girl) (protagonist)
Kiyoka (lesbian) (main)
Rika (lesbian) (supporting)

Sunu Sumu Muriku no Koibito
Naoki "Nao" Komura (bi) (protagonist)
Nono Nosaka (trans girl and bi) (main)
Kanami Shibata (bi and aro?) (supporting)
Nanako (trans man and bi) (supporting)
Nemoto-sensei (gay) (supporting)

Kaijuu ni Natta Gay
Takashi Arashiro (gay) (protagonist)
Junpei Naruse (gay) (main)
Liam (trans man) (minor)

Transgender (binary trans, non-binary, and/or intersex) manga with official English (at least partial) translations. Some of my trans labels are headcanons- those are indicated by question marks.
Organized roughly by release order in Japan.

(My definition of a trans manga is one that has a main trans character. Them being transgender may or may not be a big impact on the story.)


Not on MAL:

"Onna" toshite Idakaretai... Seitenkan Shite, Hatsukoi wo Mou Ichido./Hold Me, Baby, As a Lady... -First Love Again in the Body of a Woman.
Sanae Takahashi (trans woman) (protagonist)
Machiko (trans woman) (supporting)

Kamisama, Boku wo Koroshite Kudasai - Otoko no Karada de Umareta Jigoku/The Pain of Living in a Male Body
Subaru Kawase (trans girl) (protagonist)

Akarui/Light
Maki Sanada (trans boy) (protagonist)
*published in English release of Boys Run the Riot


I ran out of room and don't want to split this list:

Boogiepop Series
Boogiepop (genderless?) (main)

3 Partner Hajimemashita!!/We Started a Threesome!!
(name removed for spoilers) (trans woman) (main)

#DRCL Midnight Children
Luke/Lucy Westenra (genderfluid?) (main)

One-shots (one chapter stories) with transgender themes. Some are headcanons- those are indicated by question marks. Also, some are parts of anthologies.
Organized roughly by year.


Not on MAL (yet):

Natsu no Ane (2015)
Orie (trans woman) (protagonist)
*included in Yesterday wo Utatte: afterword

Chiguhagu (2016)
Tooru/Tohru (trans man) (protagonist)
Yuki (trans woman) (main)

Osananajimi Yuri (?) (2017)
College Girl (trans woman) (main)

Josei ga Suki na Josei to Otoko datta Josei no Hanashi (2019)
Makoto (trans woman) (main)

Hana Ningyou to Danna sama (2019)
Hiromi (trans woman) (protagonist)

Murai-kun wa Mizuno-kun wo Dakitai (2019)
Shion Murai (trans boy) (protagonist)
*included in Hagure Idol Jigokuhen

Akarui (2020)
Miki Sanda (trans boy) (protagonist)
*included with Boys Run the Riot

Onnanoko ni Naritai Otokonoko no Hanashi (2020)
Girl (trans girl) (protagonist)

Bokura no VR (2020)
Miharu Akina (trans boy) (main)

Watashi Ki, Oriori to (2020)
Ran Adachi (trans woman) (main)
*included with Last Gender: Nanimono demo Nai Watashitachi

Online Game de Dekita Kareshi ni Real de Aitai to Iwareta Nekama no Otoko no Ko (2021)
Miyoto (trans girl) (protagonist)

Majo ni Naritai Otoko no Ko (2022)
Koto (trans girl) (protagonist)

Doumo, Newhalf desu. (2022)
Tsukasa Andou (trans woman) (protagonist)
Maria (trans woman) (main)
Reiko (trans woman) (main)

Haru to Yakyuu (2023)
Haru (trans girl) (protagonist)

Mukashi no Osanajimi, Otokonoko Janakatta Mitai (2023)
Yuuki (trans woman) (main)


(honorable mentions- trans characters are not the main characters)

Shoujo Bigaku (Kanojo no Yuuwaku) (2006)
Yuno's Brother (trans boy) (supporting)

Unmei no Tori: Takahashi Rumiko Kessakushuu (Unmei no Tori) (2007-2011)
Mai (trans woman) (supporting)

Watashi to Watashi (Watashi to Watashi) (2009-2017)
Miyahara (trans girl) (supporting)

Onnanoko no Sekkeizu (Shounen) (2010-2012)
Miyaji's mom (trans woman) (supporting)

Shindou-ke no Jijou (2014)
Tanaka (trans woman) (supporting)