Pandrogyne was coined by Genesis P-Orridge in 1993. P-Orridge (who used s/he pronouns) described it as “a 'third-gender' and a type of gender-neutral living being more akin to the other or internal self”. S/he also said that it is not about changing the concept of gender, but rather that "pandrogeny is about neutralising gender in order to represent a future possibility for thee species". P-Orridge was a pandrogyne along with his/her partner Lady Jaye and they both went through gender-affirming surgeries in order to present in a more pandrogynous way. According to them, pandrogyny is about union and not about gender, and is different from being trans or a cross-dresser.
The flag was coined by Tumblr user beyond-mogai-pride-flags on November 18th, 2018.