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A side character, Neil, is known to the general public as a crossdressing man, but has stated canonically (although at different points) that they don't identify themselves as either a man or a woman.
Very much recommend watching the anime over reading the manga on this one
Protag is agender & intersex in a world that's slightly off from ours. A nonbinary/genderfluid intersex character is also referenced, tho cw & spoilers: that person committed suicide.
A member of the main cast says they don't really feel like a boy or a girl, in a way that gives agender or graygender kinda vibes.
The protagonist was male in a previous life but in their new life they're not human and don't have a gender, and from what I recall they're mostly just fine with that.
So it's valid to dislike the fact that all the characters in this that canonically exist outside the gender binary are non-human cryptids, but I love it anyways: they're unique, cute, beloved, and a significant portion of the cast too! Also something something the history of queer-coded monsters in media makes some queer ppl like me identify with monsters in stuff. Anyways, it's very cute!
The gender identity of the androgynous protag in this oneshot manga about IVF is never confirmed one way or another.
The main character, Erminia, is definitely more on the transmasculine side of things, but also has stated they aren't sure if they're male or female, and that they have the heart of a woman and a man. Also there's prophecies they're wrapped up in that can apply to either either twins or nonbinary/genderqueer ppl.
(cw for general ecchi problematic antics, transphobia, homophobia, incestuous feelings, sexual assault, blackmailing, kidnapping)
Shion, a prominent member of the main cast, is of indeterminate biological sex (as in: we as the audience never learn it for sure) & has a fluid gender identity.& presentation, though she more often presents herself as a woman throughout the series.
Kind of weaksauce bc the character is nonhuman and their gender is only discussed in the author's notes, but the titular incubus is confirmed by the author to be canonically genderless.
Just to preface: I could never get into this series myself, but from what I know about it this race of sentient gemstone beings, like in Steven Universe, technically don't have genders. So while they aren't human, they're technically kind of nonbinary rep? It's subjective, I'll leave it to you to decide
I want to escape from Princess education