Zenbu Kimi no Sei
All Because of You

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Quality manga with good stories which include characters that are transgender, crossdressers, body swapped, LGBT, etc.

Most manga have complex characters with substance to the stories.
Wrote a sentence for each manga that lightly describes what each one is about.

This is a list of works focusing on stories where characters experience gender or biological sex shifts as a significant part of the plot.

There is either a supernatural or major psychological component to all of these entries. Pure crossdressing works are excluded.

Comments for each entry are currently a work in progress.

Notable works that are not on MAL (yet; currently in pending approval queue):
Saki to Mika; by Sakujirou

Trans, Nonbinary, Genderqueer and other

DISCLAIMER: not every title on this list is trying to be a "good and realistic representation". But I believe even "problematic" depictions are worthy of note. You've been warned.

List of manga with non-binary characters(aka X-gender in Japan): protagonists, main characters and side characters. I tried to include only the confirmed ones.

Note: arranged in the order of release. Some of the titles are NSFW.

Work in progress!

Not found on MAL: Watashi no Kanojo wa Otoko no Ko(2018), Alien Idol(2018), Douruanki(2019).

Manga that aren't about trans characters but, like, really are about trans characters