Maria-sama ga Miteru

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Yuri/Shoujo-Ai/Girl's Love/GL Manga with binary transgender, non-binary, and intersex characters. Some of them feature a cis female/trans male relationship and shouldn't be labelled as GL.


Not on MAL (yet):

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

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

Otto wa Jitsu wa Josei Deshita
Wafuko (trans woman) (main)

Sayonara Chinchin Welcome Manman ~OL ni naritakute Seibetsu Tekigou Shujutsu shita~
Yoriko Kamikawa (trans woman) (protagonist)

Girlfriend
Kaoru Shirasaki (trans woman) (main)


Not considered GL, but GL-adjacent:

Umareru Seibetsu wo Machigaeta!
Mafuyu Konishi (trans woman)

Seibetsu X
Asuka Miyazaki (x-gender)

Hourou Musuko
Shuuichi Nitori (trans girl)

Kyou kara Yonshimai
Kashiwa Manabe (trans woman)

Densen Complex (Love Horizon)
Yuko Matsuno (trans woman)

Devilman Lady
Asuka Lan (intersex girl)

Kanojo ni Naru Hi: Another
Aya Kurokawa (male to female)

Kanojo ni Naritai Kimi to Boku
Akira Yonezawa (trans girl)

Shoujo Kakumei Utena
Utena Tenjou (genderqueer?)

More transgender girls and women in manga. I'll add more as I read more.

Part 1: https://myanimelist.net/stacks/28893
Part 2: https://myanimelist.net/stacks/29603
Part 3: https://myanimelist.net/stacks/37567