Magnolia

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DISCLAIMER: not every title on this list is trying to be a "good and realistic representation". But I believe even "problematic" depictions are worthy of note. You've been warned.

List of manga with non-binary characters(aka X-gender in Japan): protagonists, main characters and side characters. I tried to include only the confirmed ones.

Note: arranged in the order of release. Some of the titles are NSFW.

Work in progress!

Not found on MAL: Watashi no Kanojo wa Otoko no Ko(2018), Alien Idol(2018), Douruanki(2019).

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):

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)

Transgender manga without official translations but have (at least partial) fan translations in English. 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.)

Part 2: https://myanimelist.net/stacks/55113


Not on MAL (yet):

Natsu no Ane/Summer Sister (2015)
Orie (trans woman) (main)

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

Sakura-chan to Amane-kun/Sakura-chan and Amane-kun (2017)
Sakura (trans girl) (main)
Amane (trane boy) (main)

Hana Ningyou to Danna Sama/The Flower Doll Husband (2019)
Hiromi (trans woman) (protagonist)

Sayonara Chinchin Welcome Manman ~OL ni Naritakute Seibetsu Tekigo Shujutsu shimashita~/Goodbye Chinchin Welcome Manman (I Wanted to Be an Office Lady So I Had SRS) (2019)
Yoriko Kamikawa (trans woman) (protagonist)
*not fully translated

Danshi Jidai no mtf no Manga/Koukousei Hen/MTF Cartoons from the Boys' Era (2019)
Natsuki (trans girl) (protagonist)
*not fully translated

Josei ga Suki na Josei to Otoko datta Josei no Hanashi/The Story of a Girl Who Likes Girls, and a Girl Who Used to be a Guy (2019)
Makoto (trans woman) (main)

Mirai kara kita Jibun ni Onna ni naru you Settaku Sarersu Hanashi/My Future Self Is Persuading Me to Become a Woman (2020)
Yuuka (trans woman) (protagonist)

Otto wa Jitsu wa Josei Deshita/My Husband Who Actually Turned Out to Be My Wife (2020)
Wafuko (trans woman) (main)
*not fully translated

Doumo, Newhalf desu./Hi, I'm Trans (2020)
Tsukasa Andou (trans woman) (protagonist)
Maria (trans woman) (main)
Reiko (trans woman) (main)

Itsuka Shinu Shoujo/A Girl Who Will Die One Day (2020)
Yuuki Akai (trans girl) (main)

Onnanoko ni Naritai Otokonoko no Hanashi/The Story of a Boy Who Wants to Be a Girl (2020)
Girl (trans girl) (protagonist)

Ore no Karada wa Nande Onna Nanda?/Why is my Body Female? (2020)
Ryuutarou Suzumiya (trans man) (protagonist)
*not fully translated

Online Game de Dekita Kareshi ni Real de Aitai to Iwareta Nekama no Otoko no Ko/A G.I.R.L. Whose Boyfriend From an Online Game Wants to Meet Him Offline (2021)
Miyoto (trans girl) (protagonist)

Girlfriend (2021)
Kaoru Shirasaki (trans woman) (main)

Majo ni Naritai Otoko no Ko/The Boy Who Wants to be a Witch (2022)
Koto (trans girl) (protagonist)

Onna no Karada ga Iya nano de Mune o Torimashita/I Hated My Female Body, so I Cut Off My Breasts (2024)
Kazuki (non-binary) (protagonist)
*not fully translated