"It was rocky for a while," a source close to the couple told People magazine. "They did what they could to make it work."
The source said the split was amicable.
A source close to the couple told Us Weekly magazine that the couple "quietly and amicably split a few weeks ago."
The pair, who welcomed daughter Matilda in October 2005, met while they were filming "Brokeback Mountain" in 2004.
Co-stars say the chemistry was obvious from the start.
"I remember being in rehearsal, and the two of them had googly eyes with each other," co-star Jake Gyllenhaal said of the couple. "There were sparks immediately," added co-star Anne Hathaway. "It was adorable."
The Brooklyn, N.Y.-based duo welcomed their daughter during promotion for the film, with Ledger calling the former "Dawson's Creek" star the perfect mom.
But the rigorous schedule wasn't easy.
"We started promoting the movie about three weeks after [Matilda] was born, which was too soon," she said in a 2006 interview. "I'm just learning lessons now, like learning how to be a working mom."