Blue Giraffe Sports, his management company, said Wendy Goydos died Saturday morning. It said details of her death were not immediately available.
Goydos said last year that his ex-wife continued to cope with an addiction to painkillers, which led to their divorce. He was awarded full custody of his daughters in 2004, Chelsea and Courtney, when they were 13 and 11.
He took most of that season off to spend time with them at home and in the classroom, and even now builds his schedule around them by rarely playing more than two weeks in a row. Goydos took his youngest daughter with him to the British Open last year.
Goydos, a two-time winner on the PGA Tour, was on his way home from Honolulu after missing the cut in the Sony Open when he learned of his ex-wifes death.
In lieu of flowers or cards, Goydos and his family asked that donations be made to The National Headache Foundation in her name.