Bowser Jr. is son of the King Koopa himself. I am unsure if this means biological son or otherwise, but the resemblance is uncanny. Bowser also seems to be protective and emotional when dealing with Jr. as seen in the DS games, so that leads me to believe the connection is deep.
How much do we know about Jr.'s background? Does he have a mother? Is he really Bowser's son? Did he ever go by Prince Koopa? These, I must know.