The 31-year-old actress - who married the Death Cab For Cutie frontman two years ago - has decided to call time on her marriage, a representative has confirmed to US Weekly magazine.
A source said: "It was mutual and amicable. There was no third party involved."
Ben - who also fronts the band She and Him with Zooey - said in September he thought of his wife as "very beautiful".
He revealed: "I'd seen her movies and obviously I thought she was very beautiful. [When we were introduced] I was awestruck that she was even talking to me!"
Zoeey - who is a model for make-up brand Rimmel and is known for roles in films including 'Yes Man' and '(500) Days of Summer' - previously said she enjoyed marriage as it makes a relationship more concrete.
She said: "You can't expect to make no effort. You still have to make the effort and be kind and understanding. It sort of just solidifies your commitment."