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Some non-binary/x-gender manga I've read or heard about.

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


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

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 (non-binary) (protagonist)

Kyouhaku sei Shougai Chiryou Nikki
Asuka Miyazaki (non-binary) (protagonist)

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

Seibetsu Fushou ni Koi wo Shimashita.
Haru Takano (non-binary) (main)

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.

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)

Ire kawatte mo Jibun rashiku
Yuuki (trans man, gender-bending/body swapping) (main)

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.

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:

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)

Ai no Shintairiku
Sara Nikotama (trans girl) (protagonist)
Misaki (trans woman) (supporting)

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

Sunu Sumu Muriku no Koibito
Naoki "Nao" Komura (bi) (protagonist)
Nono Nosaka (trans girl and bi) (main)
Nanako (trans man and bi) (supporting)

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