The Captain is intended to be an exploration of a specific school of Postgenderism. Some people postulate that differences in the sexes themselves create inequity. Thus, if you genetically alter humans to remove differences between the sexes, you can remove the inherent inequity in society. One way is to simply remove all sexual characteristics entirely and use artificial wombs for reproduction. The other way is to give the characteristics of both sexes to all individuals, so that everyone is both male and female. The Captain is the product of a world that adopted the latter philosophy.
So, basically
@RJDiogenes is correct (although I haven't decided if the Captain will have additional genetic augmentation).
I refrained from using the term "hermaphrodite" because it's often used as a derogatory term for intersex individuals. I can't use the term "intersex" because it's simply inaccurate; The Captain is not between sexes, they are both sexes. That said, I'm certainly open to suggestions on what terminology to use.
Captain Le Guin is actually not from Earth. They're an immigrant from a distant colony, for reasons which will be revealed in the fullness of time...