The BBC Breakfast presenter, who has been appearing on the ballroom show's live tour, has three children with former sports journalist Dominic Cotton.
A statement issued by her agent 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."
The story emerged after images were published of Cotton from a dating website, where he describes himself as "separated".
Reid, who commutes from her home in south London to present BBC Breakfast from Salford, was favourite to win last year's Strictly but lost out to model Abbey Clancy in the final.
Fellow competitor Fiona Fullerton later accused her of approaching the show "with a PR campaign driven with military precision".
Reid is not the first famous name to fall foul of what has been dubbed "the curse of Strictly", with several big names suffering romantic fallouts after appearing on the show.
Her fellow contestant and Countdown star Rachel Riley announced she had left her husband just over a year after they married - and weeks after she exited the dancing show.
Boxer Joe Calzaghe paired up with dancer Kristina Rihanoff after meeting on the show in 2009, only to split up four years later.
But there have been some success stories - Kara Tointon and Artem Chigvintsev met on the show and are still together - and one wedding, when actor Jimi Mistry married his former dance partner Flavia Cacace.