In a statement released to People, representatives of the acting couple said they have been split for some time.
"In light of continuous speculation over the lives and marriage of Téa Leoni and David Duchovny, the couple has confirmed that they have in fact been separated for several months.
"The couple had hoped to keep this separation private for the sake of their children," it read.
Duchovny, 48, recently admitted himself to a rehabilitation centre seeking help for sex addiction. He returned home last week, having completed the treatment.
The X-Files actor married Leoni in 1997 and they have two children. He is due to star along with Demi Moore and Amber Heard in the comedy-drama The Joneses .