The couple, who reportedly split Tuesday, are "taking time apart" but have not decided whether to file for divorce, the website reported.
A spokesperson for Duchovny, 50, confirmed the split to E! Online.
"X-Files" star Duchovny entered rehab for sex addiction in 2008, and the couple, who married in 1997, separated for several months.
They have two children together, a 12-year-old daughter and a nine-year-old son.