"Lara and I have decided to end our marriage," Lynch said in a statement to Us. "This has been a difficult decision for us as we care very deeply about one another. We ask for privacy as we deal with this family matter."
A source told Us that Lynch recently moved out of their Laurel Canyon home in L.A.
Lynch and Embry, a psychologist, married in Sunderland, Mass., in June 2010, after meeting at a 2009 gala for the National Center for Lesbian Rights.
Embry, who is mom to daughter Haden Embry, told Vogue magazine in 2011 that it was love at first sight.
"I had stopped dating altogether. I mean, you have to sit down and think, 'How do you trust your judgment?' But I saw Jane walking in the lobby and I thought, 'I'm supposed to follow her.' It was like I'd been picked up in a fishing net," Embry told the magazine. "I was supposed to go that way -- and she was actually going the wrong way! But it was like the door was cracked. It was perfect."
Lynch, who currently stars on Broadway's Annie: The Musical, recently told Us that her stepdaughter is not that impressed by her role on Glee. "She's so unmoved by that stuff," she explained at FOX's Winter TCA Tour in January. "It's funny what kids accept kind of fast. She's not at all in awe of the fact that her mother is on TV."