The 65-year-old Microsoft founder announced the split on Twitter.
"After a great deal of thought and a lotof work, we have made the decision to end our marriage. 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 couple said in a joint statement.
"We continue to share a belief in that mission and will continue to work together at the foundation, but we no longer believe we can grow together as a couple in this next phase of our lives.
Bill and Melinda got married on New Year's Day in 1994, in a private ceremony in Hawaii.
In 2000, they launched the Bill & Melinda Gates Foundation, with ambitious goals that included the reduction of extreme poverty around the world.
This past year, it was heavily involved in the world's response to Covid-19, committing $1.75b to help develop and distribute vaccines.
The couple met in 1987, when Mrs Gates - then known as Melinda French - was a product manager at Microsoft.
In a Netflix documentary series a couple of years ago, Melinda shared an amusing anecdote from about year into their relationship, when she walked in on Bill as he was drawing up a list of the "pros and cons" of getting married.
