The theory is that his father, Prince Kusakabe didn't ascend the imperial throne although he was a Prince, which means he succeeded to the imperial throne from his mother; the Emperor, leading to the theory; Emperor Gensho is a Female-line Emperor.
父親・草壁皇子は皇太子であったが即位しておらず、天皇である母親から皇位を継承している事から、元正天皇は女系天皇であるという説である。