The actress, 52, met Lara Embry, 44, in 2009 and they exchanged vows in an intimate ceremony in Massachusetts - where same sex marriage is legal - in May, 2010. However, the couple has since decided to part ways, reported People magazine.
A statement issued by Lynch read, "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 new musical 'Annie', became a stepmother to Embry's daughter from a former relationship.
The divorce news comes less than a day after Lynch attended the Tony Awards in New York solo.