The actress, 52, met Dr. Lara Embry, 44, in 2009, and they exchanged vows in an intimate ceremony in Massachusetts, where same sex marriage is legal, in May 2010.
A statement issued by Lynch to People.com reads, "Lara and I have decided to end our marriage. 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."
Lynch, who is currently starring on Broadway in the new musical "Annie," became a stepmother to Embry's daughter from a former relationship when the couple wed, and previously gushed, "My greatest pleasure is Haden, my stepdaughter. I am surprised how much love you feel, and how you would do anything for your children."
The divorce news comes less than a day after Lynch attended the Tony Awards in New York solo.
Keep clicking for more photos of the couple during happier times ...