The couple said on Twitter they made the decision after “a great deal of thought and a lot of work on our relationship”.
In a message on the Microsoft founder’s Twitter account, the couple said they made the decision after “a great deal of thought and a lot of work on our relationship”.
Gates, the fourth richest man in the world with a net worth of $130bn (£93bn), married Melinda in January 1994.
“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,” they said.
“We continue to share a belief in that mission and will continue our work together at the foundation, but we no longer believe we can grow together as a couple in this next phase of our lives.
“We ask for space and privacy for our family as we begin to navigate this new life.”
The couple, who married on a golf course on the Hawaiian island of Lanai 27 years ago, have three children together – Jennifer, Rory and Phoebe.
They live in an earth-sheltered mansion on the side of a hill overlooking Lake Washington in Medina, Washington.
At age 31 in 1987, Gates was already the youngest billionaire ever, several years before he got married.