BJ's mother is late Queen Clawdia Koopa. She died when Bowser Jr was too young to remember her, and Bowser wont tell BJ because it would break his heart.
(this has been proven by various sources, including Nintendo magazines and that kind of stuff)
Clawdia Koopa had long, black hair and gold framed glasses. Other than that she was a girl version of Bowser.
(again, proven by a comic "Koopa's [bowser's japanise name] highschool yearbook, where she is the only member of the Bowser Fan Club)
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Do you guys remember in Yoshi's Island Luigi was captured by kamek? a stork was carrying Mario and Luigi to their parents. do you know what this mean? that's right you see the Mario universe, bowser does not need a mother to reproduce and have Bowser Jr. all the children are just carried by storks to their parents bowser's not married, Bowser Jr doesn't have a mother.
No one really knows, but the only person we ever saw with Bowser when he was young is Kamek. So everyone thinks he is a orphan.