The magazine says Wright and Penn, who have had a tumultuous relationship, have agreed to share custody of their 16-year-old son, Hopper Jack. Court papers cite "irreconcilable differences" for the split.
A representative for Wright did not return an e-mail seeking comment.
The couple married in April 1996. The Penns have twice before filed for divorce or separation only to dismiss their petition a short time later.
Sean Penn won an Oscar for his role in "Milk" at the Academy Awards in February but did not thank his wife in his acceptance speech.
Get Action News on your website
