Lynch and Sweeney had worked together on the quirky series and numerous films during the last 20 years, E! Online reported.
Lynch cited "irreconcilable differences" in the divorce petition filed Monday.
The couple has a 14-year-old son, Riley Sweeney Lynch, and is currently working together on Lynch's newest film, "Inland Empire," it was reported.
Celebrity Breakups and divorces of 2014 [PHOTOS]