Holmes' attorney Jonathan Wolfe said the two are calling it quits. The actress' publicist Leslie Sloane confirmed the divorce to Eyewitness News Friday morning.
"This is a personal and private matter for Katie and her family. Katie's primary concern remains, as it always has been, her daughter's best interest," the statement read.
Cruise's longtime entertainment attorney Bert Fields told ABC News that Holmes filed for divorce on Thursday. Another source close to the actor told the network that Holmes is asking for sole custody of their child, and that the divorce filing was a "complete surprise" to Cruise.
Cruise's publicist Amanda Lundberg told Eyewitness News that the actor is "deeply saddened" by the divorce.
"Kate has filed for divorce and Tom is deeply saddened and is concentrating on his three children. Please allow them their privacy to work this out," Lundberg said in the statement.
The plan to divorce was first reported by People magazine.
Cruise, 49, and Holmes, 33, wed in an Italian castle in 2006. The couple has a 6-year-old daughter, Suri.
Cruise and Holmes began dating a year before they wed. In May 2005, Cruise publicly declared his love for Holmes on "The Oprah Winfrey Show," emphatically jumping on the host's couch.
"Tom Cruise has always kept his life very private, even when he seems to be emotional and pouring his heart out on television," said entertainment journalist Jeanne Wolf. "And I could say the same for Katie Holmes. She's never said, 'Don't ask me about Tom,' or 'Don't ask me about my marriage.' The only thing I could say for her is anything she said about the marriage is to make it seem as loving and at the same time as normal as she could express."
The divorce news comes on the heels of great news for Cruise. He's got glowing reviews for his musical roll in "Rock of Ages."
"Tom Cruise is the more powerful of the two, so I don't imagine he's going to lose many friendships in Hollywood. And I don't have a feeling that either one of them has close private friends. I think their life was very fenced in, very closed," said Wolf.
Cruise, known for his roles in "Top Gun" and the "Mission Impossible" films, was previously married to Mimi Rogers and Nicole Kidman, with whom he has two children. This was the first marriage for Holmes.
Holmes appeared to have filed for divorce anonymously, which is legal in New York. Cruise's rep is asking for privacy for the two to work things out.
ABC News and the Associated Press contributed to this report.