I noticed in my post “Most hated clichés in BL and GL series” that one of the things people dislike is that most GL series are slice-of-life about school age girls and that transgenders and genderfluid and nonbinary people aren’t represented, so I wrote this list about all the GLs that belong to different genres and all the series that have transgender or genderfluid or nonbinary protagonists I know.
If you know other series like these, feel free to talk about them.

GL SERIES
Fantasy
Manga
-“Medusa” by Ryouko Yamagishi
-“Hatshepsut” by Ryouko Yamagishi
-“Hana calendar” by Nagori Yuu
-“Okisaki-sama to ningyohime no ohanashi” by Shinoa
-“She becomes a tree” by Pageratta
-“Sakura no ki no kami-sama” by shiuriri
-“Candy moon” by Mira
-“Fushigi no kuni no Miyuki-chan” by CLAMP
-“Kimi ga shinu made koi wo shitai” by Aono Nachi
-“Watashi o tabetai, hitodenashi” by Naekawa Sai
-“Kinoko ningen no kekkon” by Murayama Kei
-“Mahou shoujo Oriko magica”, “Mahou shoujo Oriko magica- Betsu hen” and “Mahou shoujo Oriko magica- Sadness prayer” by Magica Quartet (part of the “Puella magi Madoka magica” franchise and it’s a franchise that I suggest because the characters are interesting and the relationships between the girls, both the romantic and the platonic ones are well-written)

Manhwa
-“Moonlight garden” by Kang Unnie and MissPM
-“On a leash” by Aji

Manhua
-“Lin Yao Lu” by Shi Yi Er
-“Harp and poetry under the aurora” by Oku Miao
-“Fall in love with the empress” by Chinese authors whose names I don’t know because I found them only written in Chinese and I don’t know the language

Comics
-“Monstress” by Marjorie Liu and Sana Takeda
-“RED” by teloka
-“Let’s celebrate” by teloka
-“High class homos” by momozerii
-“Mage & Demon queen” by Color LES
-“Sirenita” by Fran
-“The legend of Korra- Turf wars” by Irene Koh and “The legend of Korra- Ruins of the Empire” by Michelle Wong (they are the sequel to the animated series “The legend of Korra” by Michael Dante DiMartino and Bryan Konietzko and the romantic relationship between Korra and Asami plays a big role in them. I suggest to everyone to read and see every part of the “Avatar- The last airbender”/“The legend of Korra” franchise because the worldbuilding is great, the magic system is written excellently and the characters are interesting)

Novel
-“Female general and eldest princess” by Please don’t laugh
-“Clear and muddy loss of love” by Please don’t laugh
-“Matrilocal marriage” by Please don’t laugh
-The locked tomb” series by Tamsyn Muir
-“The burning kingdoms” series by Tasha Suri
-“In the Vanishers’ palace” by Aliette de Bodard
-“Fireheart tiger” by Aliette de Bodard
-“Girl, serpent, thorn” by Melissa Bashardoust (the protagonist is bisexual and finds herself in a love triangle between a boy and a girl and she chooses the latter)
-The short story “A dead Djinn in Cairo” and “A master of Djinn” by P. Djèlí Clark (they are part of the “Dead Djinn universe” and I suggest you to read all the stories set in it because the author mixed Coptic Christianity, Islamic mythology, modern Egypt culture and Ancient Egyptian mythology with mystery, alternate history, urban fantasy and steampunk perfectly)
-“She who became the sun” by Shelley Parker-Chan
-“Light from uncommon stars” by Ryka Aoki
-“Sappho’s leap” by Erica Jong (the protagonist is bisexual and her relationships with both men and women play a big role in the plot)
-“Kissing the witch” by Emma Donoghue
-“The saga of the Renunciates” by Marion Zimmer Bradley (part of the “Darkover” saga and I suggest to read all the books because the worldbuilding and the magic system are excellent and the narrative deconstructs the sexism, the misogyny and the homophobia present in ‘60s, ‘70s and ‘80s fantasy and science fiction)
-“Lythande” by Marion Zimmer Bradley (spoiler! The protagonist is a butch lesbian who hides her true gender because it’s the condition for her magic powers as all the mages of her order have to respect a specific condition of their pact to get their powers)
-“The rise of Kyoshi” and “The shadow of Kyoshi” by F. C. Yee (the protagonist is bisexual and she ends up with her female best friend. The novels are part of the “Avatar- The last airbender/The legend of Korra” franchise by Michael Dante DiMartino and Bryan Konietzko)

Animation
-“Revolutionary girl Utena” by Be-Papas
-“Simoun” by Studio Deen
-“Puella magi Madoka magica” and “Puella magi Madoka magica- The rebellion story” by Magica Quartet (part of the “Puella magi Madoka magica” franchise)
-“The legend of Korra” by Michael Dante DiMartino and Bryan Konietzko (it’s the sequel to “Avatar- The last airbender” and the protagonist, Korra, and Asami are both bisexual women and how they pass from love rivals to friends to lovers is one of the plots of the series)

Science fiction
Novel
-“This is how you lose the time war” by Amal El-Mohtar and Max Gladstone
-“Teixcalaan” duology by Arkady Martine
-“Seven of infinities” and “The red scholar’s wake” by Aliette de Bodard (part of the Xuya universe. I suggest you to read all the stories set in this universe because it’s a perfect example of alternate history and space opera inspired by Vietnamese culture and the characters are interesting)

Historical
Manhwa
-“Her Shim-Cheong” by Seri and Bi-wan
-“Blind passion” by Hyun Eun-mi and Sohn Gaepi
-“Opium” by Aji

Manhua
-“Shuang jing” by Li Zongchen and noftB

Novel
-“The color purple” by Alice Walker

Thriller
Manga
-“Gunjou” by Ching Nakamura

Manhwa
-“Vengeance” by Aji

Manhua
-“I’m more dangerous than you” by An De

Horror
Manga
-“Happy sugar life” by Tomiyaki Kagisora

Novel
-“Carmilla” by J. Sheridan Le Fanu

TRANSGENDER
Manga
-“Claudine!…” by Ryouko Ikeda (beware, it’s a tragedy)
-“Wandering son” by Takako Shimura
-“Bokura no hentai” by Fumi Fumiko (one of the protagonists is a trans girl)

Comics
-“Magical boy” by The Kao (the protagonist is a trans gay boy)
-“Lumberjanes” by ND Stevenson, Grace Ellis, Shannon Watters and Gus Allen (one of the protagonists, Jo, is a trans girl)

Novel
-“Light from uncommon stars” by Ryka Aoki (one of the protagonists is a trans woman)
-“Cemetery boys” by Aiden Thomas (the protagonist is a trans gay boy who ends up in a relationship with a cisgender boy)

GENDERFLUID AND NONBINARY
Manga
-“Marginal” by Moto Hagio (the protagonist Kira is defined a boy only because s/he was found by men who belong to a single gender society: Kira is a hermaphrodite and has both a female and male soul)
-“RG Veda” by CLAMP (the protagonist, Ashura, is stated to have no gender)
-“Love me for who I am” by Kata Konayama (one of the protagonists is a nonbinary person assigned male at birth and ends up to be the love interest of another of the protagonists, a cisgender boy)

Novel
-“The Tensorate” series by Neon Yang is set in a world where people are born without a gender and they decide which one they feel to belong when they’re teens. The themes of gender, genderfluidity and sexuality play a big role in the plot and one of the main characters is nonbinary
-“The Singing hills cycle” series by Nghi Vo has a nonbinary wandering cleric as its protagonist