Yes, in the onsens you don't wear anything but they are strictly separated, men and women.
As an aside, many years ago I was in one in Chiba with a colleague when about twenty heavily tattoed men arrived together. They stood and stared menacingly at the people already there and we all decided it was a good time to leave!
I asked my colleague who they were and why we all felt obliged to leave.
They are Yakuza (Japanese mafia) he said and leaving wasn't going to be optional.
ford family