The actor is seeking joint physical and legal custody of their children, daughter Dylan, 18 and son Hopper, 15. He is also requesting that the court not award any spousal support to Wright Penn. The papers show the couple separated on April 23.
Penn, 48, and Wright Penn, 43, started divorce proceedings in Marin County Superior Court in December 2007 after 11 years of marriage.
But they put the brakes on their divorce action four months later when a court clerk dismissed the divorce petition at their request.
During their separation, Penn stepped out with model Petra Nemcova at an L.A. Oscar party and nightclub.
Oscar OmissionPenn raised eyebrows earlier this year when he neglected to thank his wife during his Oscar acceptance speech (he took home the best actor award for his portrayal of politician and gay rights activist Harvey Milk). After the ceremony, Penn, with his wife by his side, explained the omission to Access Hollywood: "She knows," he said. Wright Penn elaborated, saying they knew there wouldn't be "enough time."
The couple began dating in the early '90s, following his divorce from Madonna in 1989, and married in 1996. They have also starred together in several films, including 1998's Hurlyburly and 1997's She's So Lovely.
"Marriage ain't easy, but it's great most of the time," Penn told Entertainment Weekly in 1997. "I love Robin. I've always loved her."
Calls to Penn's rep have not been returned.
Extra first broke the news of Penn's filing for separation.