The couple's rep confirmed the news to Us Weekly in a statement shared Wednesday.
"Evan Rachel Wood and Jamie Bell have decided to separate," the statement read. "They both love and respect one another and will of course remain committed to co-parenting their son. This is a mutual decision and the two remain close friends."
Wood, 26, and Bell, 28, met on the 2004 set of Green Day's music video "Wake Me Up When September Ends." The two later began to date, got matching tattoos of each others' initials and ended their relationship in 2006. The pair reconciled five years later and married in October, 2012. They welcomed a son in July 2013.
"They love each other so much but it just wasn't right," a source close to the couple said of their breakup.