Sayonara Daisy: Mayuzuki Jun Shoki Tanpenshuu

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Even more transgender girls and women from manga. Some are headcanons- those are indicated by question marks.

Part 1: https://myanimelist.net/stacks/28893
Part 2: https://myanimelist.net/stacks/29603
Part 4: https://myanimelist.net/stacks/46068

More manga featuring LGBT (gay, lesbian, bisexual, binary transgender, non-binary, genderqueer, intersex, queer, pansexual, asexual, aromantic, etc.) characters in non-BL/non-GL manga. Some are headcanons- those are indicated by question marks.

Part 1: https://myanimelist.net/stacks/37019


Not on MAL (yet):

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

Akarui
Maki Sanada (trans boy) (protagonist)

Chiguharu
Tooru/Tohru (trans man) (protagonist)
Yuki (trans woman) (main)

Gay Fuuzoku no H Jijou
Kazuaki (gay) (protagonist)
Nori (gay) (main)

Girlfriend
Megumi Makimura (bi) (protagonist)
Kaoru Shirasaki (trans woman) (main)

Itsuka Shinu Shoujo
Yuuki Akai (trans girl and lesbian?) (main)

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

Ore no Karada wa Nande Onna Nanda?
Ryuutarou "Ryuu" Suzumiya (trans man) (protagonist)

Otto wa Jitsu wa Josei Deshita
Tsushima Tsushima (pan) (protagonist)
Wafuko Tsushima (trans woman and queer) (main)

Sayonara Chinchin Welcome Manman ~OL ni Naritakute Seibetsu Tekigo Shujutsu shimashita~
Yoriko "Yoripi" Kamikawa (trans woman and lesbian)

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):

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)

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)

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)

pretty self-explanatory.
Manga from the alternative manga magazine Manga Erotics F that have been officially published in English. Since Comic Beam has a broader audience than most alternative manga magaziness, it's arguable whether it should be considered one, but I still included it. It would be updated every time a new one is announced/comes out. Hope to update it as many times as possible!!
If I forgot something, please let me know.

If there are any other magazines you would like me to do this for, please let me know. Would love to know if you make some lists like this yourselves, I would add them to the links!

Links - Stacks for alt manga from other magazines:
AX - https://myanimelist.net/stacks/62676
Comic Beam - https://myanimelist.net/stacks/62679
Comic Cue - https://myanimelist.net/stacks/62678
Garo - https://myanimelist.net/stacks/62675
Ikki - https://myanimelist.net/stacks/62680
Manga Erotics F - https://myanimelist.net/stacks/62682
Torch - https://myanimelist.net/stacks/62677