A rep for the actor confirmed the news to Us Weekly.
"They remain good friends," his rep told the mag.
A source claims the couple, both 32-years-old, separated two months ago.
Van Der Beek and McComb married in July 2003.
McComb reportedly met Van Der Beek through her sister Jennifer McComb, who guest starred on "Dawson's Creek" in the late 1990's.
Related Content from AccessHollywood.com:
VIEW THE PHOTOS: Surprising Former Couples
PLAY IT NOW: Katie Holmes Gets 'Independent' In NYC (April 26, 2009)
PLAY IT NOW: Victoria's 'Spicy' Lingerie Fashion Show: Arrivals, Part I