The couple made the announcement on the Amazon chief executive's Twitter account.
"As our family and close friends know, after a long period of loving exploration and trial separation, we have decided to divorce and continue our shared lives as friends," the couple said in the joint statement.
"We feel incredibly lucky to have found each other and deeply grateful for every one of the years we have been married to each other. If we had known we would separate after 25 years, we would do it all again," the statement continued.
CNN reported that Jeff Bezos, 54, met MacKenzie, 48, at the New York hedge fund D.E. Shaw, before they moved to Seattle where Bezos started Amazon. Jeff Bezos is worth $137 billion, the Bloomberg Billionaire Index reported.
MacKenzie Bezos is a novelist who has written numerous books, including Traps and The Testing of Luther Albright. The couple has four children -- a daughter adopted from China and three sons.
"We've had such a great life together as a married couple, and we also see wonderful futures ahead, as parents, friends, partners in ventures and projects, and as individuals pursuing ventures and adventures," the joint statement said.
"Though the labels might be different, we remain a family, and we remain cherished friends," the statement ended.
Last September, the couple announced they would give $2 billion to a fund called "Bezos Day One Fund," which will support non-profits that assist homeless families and create a preschool network in low-income communities.
In January 2018, they said they would give $33 million in scholarships to students connected with the Deferred Action for Childhood Arrivals program known as Dreamers since they are not eligible for federal financial aid.
The divorce comes on the heels of Amazon's big news in November that it would create a new headquarters in New York City and suburban Washington, D.C., bringing thousands of new workers to the area in the coming years.