Shia and Mia exchanged vows in an Elvis-themed wedding in Las Vegas in October, 2016, with their mothers as witnesses, but it appears the romance is over, according to his representative.
"Shia and Mia have filed for divorce," a statement reads. "The separation is amicable and all details pertaining to the divorce proceedings will remain private."
The former couple met and fell in love while shooting "Nymphomaniac" in 2012.
The stars split in 2015 after the "Transformers" star was caught on tape threatening Mia during a street fight in Germany. They reunited and reports suggested LaBeouf had proposed in early 2016.
Shortly after tying the knot, Shia confessed marriage had changed him for the better, telling E! News in December, 2016, "I've been lied to my whole life. You always hear these people who are all cynical, like, 'Ah, man, once you get married everything changes.' But for the better though!"
The divorce news comes on the back of reports linking LaBeouf to his "Honey Boy" co-star, FKA Twigs, who previously dated Twilight star Pattinson.
The Daily Mail obtained recent photos of the couple together in London. Twigs, real name Tahliah Debrett Barnett, recently worked with LaBeouf on the upcoming film, which he wrote.
Pressed to comment on the nature of her relationship with Shia, the 30 year old told the newspaper, "We're very happy, we're having a nice time."
The singer and artist was previously engaged to Pattinson - her boyfriend of three years. They split in October (17).