Kim Wahlberg cited "irreconcilable differences" in her filings in Los Angeles Superior Court. Donnie Wahlberg's petition was filed in Ventura County.
The couple were married in August 1999 and separated earlier this year.
The move comes as Wahlberg, 39, prepares to tour with a reunited New Kids on the Block and appears on the big screen in "Righteous Kill," which will be released on Sept. 12.
The former couple have two sons, ages 15 and 7.