The former Detroit Lions star submitted the paperwork in Oakland Circuit County Court on Friday, according to the Detroit Free Press.
The newspaper reports that a "breakdown in martial relations" was listed on the petition. Sanders is seeking joint custody of the couple's three young boys, ages 10, 8 and 4.
He has another son, Stanford running back recruit Barry Jr., from another relationship.
Sanders married the former Lauren Campbell in November 2000, one year after his surprise retirement from the NFL. She was a weekend news anchor at Detroit's NBC affiliate and a former model. Their wedding was a private affair that had only 50 guests and drew minimal attention from the press. Barry didn't invite his father to the ceremony, reportedly due to a falling out they had after the son's abrupt retirement.
Barry and Lauren had their first son, Nigel, nine months after the wedding.
Sanders played 10 years for the Detroit Lions, winning four rushing titles and finishing his career as the second all-time leading rusher in league history. Only his father's hero, Jim Brown, averaged more rushing yards per game.
Sanders was elected to the Pro Football Hall of Fame in 2004.
