The 48-year-old actress and 52-year-old actor confirmed Thursday in a joint statement to People that they are calling it quits after more than a decade together.
"James and I have shared a great life together and have many wonderful memories. We've enjoyed working together, most recently on The Brave, where he joins us for our two mind-bending finale episodes," the pair said.
"Relationships change and grow; we're taking time for that," they added. "We care very much for each other and plan to continue raising our two beautiful boys in love and harmony. Thank you for allowing us privacy as our family evolves."
Heche and Tupper started dating in 2007 after meeting on the set of the ABC series Men in Trees, and welcomed their first child, son Atlas, in 2009. The actress is also parent to 15-year-old son Homer with ex-husband Coleman Laffoon.
Us Weekly reported Heche has filed a petition to establish custody and child support for Atlas. The star is seeking joint custody and "reasonable visitation" rights for both parents, in addition to legal fees from Tupper.
Heche previously dated television personality Ellen DeGeneres. She co-starred on the Syfy series Aftermath with Tupper, who is known for portraying David Clarke on Revenge and Nathan Carlson on Big Little Lies.