"Evan Rachel Wood and Jamie Bell have decided to separate," their rep said.
Evan and Jamie in 2013
"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."
Speaking to Us Weekly, a source added: "They love each other so much but it just wasn't right."
Jamie and Evan first met in 2004 when they starred in a music video for rock band Green Day. They later split but reunited in 2011 before confirming the following year on Twitter they had indeed become husband and wife.
In October 2013, the couple exchanged messages on the social networking site to celebrate their one-year anniversary.
"It's been 12 months since I told someone how much I loved them. I'm forever thankful they chose me. Happy Anniversary @evanrachelwood XXX," wrote Jamie.
"Happy anniversary @1jamiebell! You are the best husband and father anyone could ask for. Here is to many more adventures ahead. I love you x," replied Evan.
Jamie appeared to have deleted his account as of Wednesday while Evan, who still described herself as Mrs. Bell, tweeted: "Twitter break for a while. ...to be continued."