Manga that explore Gender Identity

It's manga about a group of NEET women and a crossdressing guy who start making clothes together. The reason why it's on this list is the crossdressing guy, who since he was a little boy has a liking for feminine clothes, so when he was about to finish high school he started crossdressing, and continued doing so during his college life. He is cis, but I think it's really nice to have a man who is sure about his gender crossdressesing, and being respected and never made fun of in the story.

It's a harem manga. Not my style, but the trans rep isn't the worst. Yuki, the main girl, is trans, and starts living with Masato. She believes he is the boy she made a promise with years ago and is in love with him. As they start living together, other girls show up in Masato's life, like any harem manga with ecchi. I suppose it's not bad for the genre, since the ecchi doesn't revolve around harrassment, so I decided to add it here in case anyone is interested. TW: misgendering, homophobia.

Masahiko lost both his parents and now he started living with relatives: his mother's sister, a trans woman, and her husband, a trans man! They also have a daughter. This is a slice of life manga that follows the lives of the members of this family. It's a 90s manga so it has some outdated ideas and language.

TW: misgendering, transphobia, homophobia, use of the word "transvestite".

The story of friendship between a trans boy and a crossdressing boy. Unfortunately this manga is on hiatus, but the few chapters that are out are a fun read.

tw: misgendering

This manga is about a group of people who work in a cafe. The main character is a non-binary person, that despite having a male body likes to wear feminine clothes and is not a boy nor a girl. There's also binary transgender characters as well as crossdressers in the story.

tw: misgendering, internalized homophobia.

This manga's plot is not surrounded by transgender themes. It's a mystery/horror manga that happens to have a transgender character introduced on volume 5, and she stays and has a decent ending on volume 6. I didn't expect it and it was nice, a decently written trans character in a mystery manga.

tw: homophobia, misgendering.

Arima is a boy who has a lot of gender issues due to the fact that he was raised as a girl when he was a child. Taiga falls in love with him thinking he was a girl, but soon he learns the truth.

TW: child sexual abuse, rape, misgendering.

When Richard was born, his mother and the ones surrounding them, believed he was the spawn of the devil. Richard grew up believing he was cursed and would bring misfortune to his family. All this because his body is neither male or female, having characteristics of both sexes. As he grows older, he wants to help his father to become king. We follow his story.

TW: sexual assault, violence, sexism

Otomen is a manga about how being feminine or being masculine doesn't define your gender. The protagonist, Asuka, is an "otomen", a man with "feminine" interests. He starts dating Ryo, a girl who is good at fighting and other "masculine" activities, while being bad ar "feminine" things. We follow their lives and of their friends. An actual trans character is revealed much later in the story.

TW: transphobia, sexism/misogyny

This is a short manga about a boy who enjoys dressing like a girl and a girl who dresses like a boy. It's short so there isn't a lot of development, but it's really cute and talks about how your gender doesn't matter and you should wear what you like no matter if you're a boy or a girl.