Lynch, 52, and clinical psychologist wife Lara Embry, 44, met at a fundraiser in San Francisco in 2009. They got engaged and were married in 2010 on Memorial Day in a small ceremony in Massachusetts, where same sex marriage is legal.
The "Glee" star said that the divorce was "a difficult decision for [them] as [they] care very deeply about one another."
During their marriage, Lynch became very close to Embry's daughter Haden.
"My greatest pleasure is Haden, my stepdaughter," Lynch said in April. "I am surprised how much love you feel, and how you would do anything for your children."
Lynch is busy starring as Miss Hannigan in "Annie: The Musical" on Broadway. She performed a number from the musical for the Tony Awards on Sunday.
The couple does not have a prenuptial agreement and will be required to split their assets 50/50. A California judge is likely to dissolve the marriage. Although gay marriage is not legal in California, the state does recognize legal out-of-state same sex marriages when performed in states where gay marriage is legal.