Watashi no Suki na Senpai

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More transgender boys and men in manga.

Part 1: https://myanimelist.net/stacks/28861

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)

Kaoru-san no Kikyou (Senpai)
Shirafuji (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?)

Gender-bending (sex changing through supernatural methods) characters who turn out to like their new gender and come out as transgender. Some are debatable.

One-shots (one chapter stories) with transgender themes. 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)

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

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)

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