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Mangas in which one or more of the main characters are trans.

A list of some manga and one-shots that focus on one's gender identity

As a disclaimer, it's important to understand that unfortunately, there are very few manga that actually comment on gender identity issues, and sadly, the manga that try to tackle these topics are not the greatest in terms of quality.

The manga are listed from best to worst, in my perspective, with Hanayome wa Motodanshi being the "line" at which I'd actually recommend the manga. I have also included my review of how well I felt the story and topics were handled as well as potential triggers as a warning.

Also, note that some series that I included are disconnected anthology manga that I have not read in their entirety.
Extra note, I would love to add more but after 18 different entries I'm all gendered out.

Non-Mal comics/manga:

Sakura-Chan to Amane-Kun| by Asazuki Norito |7|
(Very short read that seems to be discontinued? I'm not sure about the status of the manga, but what's there is really good and enjoyable. It's just sad that it's unfinished.)

Is It Strange To Feel Dysphoric After Coming Back From An Isekai?!| by squipkechi |7|
(Pretty short and not very deep, but was a very pleasant read)

The Story of a Girl Who Likes Girls, and a Girl Who Used to be a Guy| by Masada Yuu |7|
(Extremely short and not deep at all, but I still found it to be very cute)

Manga with transgender girls/women. Some are headcanons- those are indicated by question marks.


Part 2: https://myanimelist.net/stacks/29603
Part 3: https://myanimelist.net/stacks/37567
Part 4: https://myanimelist.net/stacks/46068


Not on MAL (yet):

"Onna" toshite Idakaretai... Seitenkan Shite, Hatsukoi wo Mou Ichido.
Sanae Takahashi (trans woman) (protagonist)
Machiko (trans woman) (supporting)

Kamisama, Boku wo Koroshite Kudasai - Otoko no Karada de Umareta Jigoku
Subaru Kawase (trans girl) (protagonist)

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

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

Watashi, Danshikou Shusshin Desu. Comic
Ayana Tsubaki (trans woman) (protagonist)

Umanbo!
Manko Ushida (trans woman) (protagonist)

Otomeza no Jun
Jun (trans woman) (main)

Mirai kara kita Jibun ni Onna ni naru you Settaku Sarersu Hanashi
Yuuka (trans woman) (main)

Danshi Jidai no mtf no Manga/Koukousei Hen
Natsuki (trans girl) (protagonist)

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

Natsu no Ane
Orie (trans woman) (main)

Itsuka Shinu Shoujo
Yuuki Akai (trans girl) (main)

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

Massugu Aoide
Aoi (trans girl) (main)

Oppai wo Totta Kareshi.
Aoi Ishikawa (trans girl) (main)

Barcode Fighter
Sakura Arisugawa (trans girl) (main)

Chiguhagu
Yuki (trans woman) (main)

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

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

Woman with Flowers
Jae-Hee (trans woman) (main)

Girlfriend
Kaoru Shirasaki (trans woman) (main)

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

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

Hana Ningyou to Danna Sama
Hiromi (trans woman) (protagonist)

Yasashii Rival
Marika (trans woman) (main)

Haru to Yakyuu
Haru (trans girl) (protagonist)

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

Tonari no Trans Shoujo-chan (Taihai Tekina Trans-chan)
Aikawa (trans girl) (main)

Tonari no Trans Shoujo-chan (Otouto wa Trans-chan)
Ayumu (trans girl) (main)

Tonari no Trans Shoujo-chan (Mirai kara Kita Trans-chan)
Yuuka (trans girl) (protagonist)

Tonari no Trans Shoujo-chan (Nitsukawashii Trans-chan)
Yoshi (trans girl) (main)

Ore no Kanojo wa Kawaii Darouga
Bom (trans woman) (main)

Untitled Flowers: Tamago wo Umanai Watashitachi
Akane (trans woman) (main)

Tonari no Shibafu ga Aosugiru
Aya (trans girl) (main)

Yuri/Shoujo-Ai/Girl's Love/GL Manga with binary transgender, non-binary, and intersex characters. Some are headcanons- those are indicated by question marks.
Also, 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)

Yurige no Heroine ni Tensei Shita Ore, Nazeka Are ga Haeta Mama desu
Hikaru Sawatari (trans girl) (protagonist)

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

Date Aite ga Ikemen ♀ Datta Ken
Ushio Toudou (non-binary) (main)

Atto Iu Man ni Wasureru (Namae no Hanashi)
Akane (non-binary) (protagonist)
*this particular story isn't GL, but the others are


Not considered GL, but GL-adjacent (some also not on MAL yet):

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)

Umareru Seibetsu wo Machigaeta!
Mafuyu Konishi (trans woman) (protagonist)

Seibetsu X
Asuka Miyazaki (x-gender) (protagonist)

Hourou Musuko
Shuuichi Nitori (trans girl) (protagonist)

Kyou kara Yonshimai
Kashiwa Manabe (trans woman) (main)

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

Kaoru-san no Kikyou (Senpai)
Shirafuji (trans woman) (main)

Ohana Holoholo
Maya Nagumo (trans woman?) (protagonist)

Devilman Lady
Asuka Lan (intersex girl) (main)

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

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

Girlfriend
Kaoru Shirasaki (trans woman) (main)

Shoujo Kakumei Utena
Utena Tenjou (genderqueer?) (protagonist)

Versailles no Bara
Oscar François de Jarjayes (genderqueer?) (main)

Silkscreen
They (genderfluid or trans man) (main)

Mahou Shoujo Madoka★Magica
Kyuubey (genderless) (main)

Concept Café-jou wa Koi wo Kiru
Tao (trans woman) (supporting)

Double House
Maho (trans woman) (protagonist)
Koko (trans woman) (supporting)

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

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


Not on MAL (yet):

Atto Iu Man ni Wasureru (Namae no Hanashi)/Things Easily Forgotten (About Names) (2013)
Akane (non-binary) (protagonist)

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

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

Date Aite ga Ikemen ♀ Datta Ken (2023)
Ushio Toudou (non-binary) (main)

Tonari no Trans Shoujo-chan (Taihai Tekina Trans-chan) (2025)
Aikawa (trans girl) (main)

Tonari no Trans Shoujo-chan (Otouto wa Trans-chan) (2025)
Ayumu (trans girl) (main)

Tonari no Trans Shoujo-chan (Mirai kara Kita Trans-chan) (2025)
Yuuka (trans girl) (protagonist)

Tonari no Trans Shoujo-chan (Nitsukawashii Trans-chan) (2025)
Yoshi (trans girl) (main)

Boys Run the Riot: In Transition
Ryou Watari (trans man) (protagonist) (2025)
*sequel to Boys Run the Riot


(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)