Mr Johnson and his wife said they separated “several months ago” after deciding it was in their “best interests” to split. The couple are now in the process of divorcing.
The statement said: “Several months ago, after 25 years of marriage, we decided it was in our best interests to separate.
“We have subsequently agreed to divorce and that process is under way.
“As friends we will continue to support our four children in the years ahead. We will not be commenting further.”
The statement comes after The Sun reported that the former foreign secretary was no longer living with his wife, amid allegations of him cheating on her.
The pair are believed to have split around the time that they left the Carlton Gardens grace and favour house, following Mr Johnson’s resignation as foreign secretary in July over Theresa May’s Chequers Brexit proposals.
The divorce announcement follows allegations of a third affair.
The Uxbridge MP has previously been accused of affairs with writer Petronella Wyatt and art consultant Helen Macintyre, who was said to have given birth to Mr Johnson’s child.
And Mr Johnson’s daughter Lara has told friends that the Conservative MP is a “selfish b******”, according to The Sun.
She said: “Mum is finished with him. She will never take him back now.”
And a friend of Mr Johnson reportedly said: “He hates the children knowing this stuff but there’s no getting around the fact that his living arrangements have changed. It’s all very painful to watch.”
Mr Johnson and his lawyer wife, both 54, married in 1994 and have four children.
The Brexiteer, who served two terms as London mayor, had been tipped to be the next leader of the Conservatives.
Mr Johnson won the latest Conservative Home poll of who should be the next leader of the party with 35 per cent of the votes, prior to the divorce announcement.
Home secretary Sajid Javid came second with 15 per cent of the votes.