Watson cited irreconcilable differences in papers filed by her lawyer on Monday in Los Angeles Superior Court. She is seeking spousal support and joint legal and physical custody.
Bonds, major league baseball's home run leader, is awaiting trial after pleading not guilty to lying to a federal grand jury in December 2003 when he denied knowingly taking performance-enhancing drugs. The trial has been delayed because of a dispute over admissible evidence.
Although he told Giants fans last season during an appearance at AT&T Park that he was "not retired," Bonds has not played an inning of professional baseball since the fall of 2007.
Bonds' first marriage to Susann Margreth Branco ended in a highly publicized divorce in 1994.