In a joint statement posted to their respective Twitter accounts, the pair said the breakup comes after reaching a mutual decision that they could no longer "grow together as a couple in this next phase of our lives."
"After a great deal of thought and a lot of work on our relationship, we have made the decision to end our marriage," the couple said.
Bill and Melinda Gates established a private philanthropic foundation bearing their names in 2000 which has concentrated on funding health research, much of it in the world's poorest nations.
"Over the last 27 years, we have raised three incredible children and built a foundation that works all over the world to enable all people to lead healthy, productive lives," the statement read.
Bill Gates is the fourth-wealthiest person in the world, according to a tally kept by Forbes Magazine, which lists his net worth at $124 billion, thanks in part to Microsoft stock.
The Bill and Melinda Gates Foundation, led by CEO Mark Suzman, is under the direction of the couple and fellow billionaire Warren Buffett. It has 1,600 employees and a trust endowment of nearly $50 billion.