"I can confirm that Travis filed this morning," Barker's rep, Dvora Vener, told PEOPLE.
Through her publicist, Moakler told PEOPLE, "My only concern right now is for the welfare and best interests of my children."
Barker, 30, plays drums for the band the Transplants as well as for blink-182, which is on indefinite hiatus. Moakler, 31, is a former Miss USA who has appeared in films including Big Momma's House 2 and Pauly Shore is Dead.
They were married in a Gothic, Nightmare Before Christmas-inspired ceremony on Halloween eve in 2004 and have two children: son Landon, 2, and daughter Alabama, 7 months. Moakler also has a daughter, Atiana, 7, with her ex-fiancé, boxer Oscar de la Hoya.
The couple's wedding and life as a family were captured by MTV cameras for the reality show Meet the Barkers, which premiered in April 2005.
In early July, they put their 12,000-sq.-ft. Tuscan villa in Bel Air, Calif., where much of the series was filmed, on the market for $8.5 million.