The X-Files actress and Griffiths recently ended their relationship, though they plan to remain friendly for the sake of their two children, reports US Weekly.
"Gillian Anderson and her partner Mark Griffiths have amicably separated after six years together," a spokesperson for Anderson told the publication.
The couple are parents to two sons, 5-year-old Oscar and 3-year-old Felix. Anderson also has a 17-year-old daughter called Piper from her first marriage to Clyde Kotz.
Anderson's second marriage to documentary maker Julian Ozanne lasted two years. She and Griffiths never married.
The 43-year-old was recently cast in I'll Follow You Down, a new sci-fi film also starring Haley Joel Osment and Rufus Sewell.