The court papers, filed in Santa Fe, N.M., claimed a "state of incompatibility exists between the two parties," according to the news agency.
"Elizabeth and Randy Travis have agreed to part ways. Elizabeth will remain Mr. Travis' personal manager," the couple's rep said in a statement. "They do not intend to comment any further and ask for your respect for their privacy during this time."
Randy, 51, and Elizabeth married in secret in 1991 after dating for more than 10 years.