BBC Breakfast presenter Susanna, who appeared on the last series of Strictly, has three sons with Dominic and says they remain "good friends".
The news comes after it emerged Dominic had created a profile on a dating website, marking his relationship status as 'separated'.
In a statement, Susanna's rep said: "Susanna Reid and Dominic Cotton have agreed to separate but remain good friends.
"The welfare of their children remains paramount for both of them at this time. Please respect their space and privacy."
Susanna, 43, has been in a relationship with 46-year-old Dominic, who is chief executive for a children's charity, for 15 years and they live in south London.
Since the BBC headquarters moved to Manchester, Susanna has spent much of her time travelling up and down the country for work. Her workload was also doubly hectic before Christmas due to Strictly rehearsals.
In December, Dominic said: "Her schedule has been really full-on. We knew it would be an enormous commitment but we discussed it and I was so happy to back her to do it."
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