In a joint statement released to multiple outlets, the couple said: "We can confirm that we have separated and have been for some time. We do however continue as great friends with the utmost respect for one another. We ask for our privacy during this time."
The former duo first met while working together on the 2011 film Season of the Witch. They married in 2014, and welcomed their first child together one year later -- daughter Ivy Rose.
Claire, who took home a Golden Globe and Screen Actors Guild Award for her role as Queen Elizabeth II on The Crown, recently opened up about leaving the show after its second season.
"As an actor, there's nothing worse than the sound of 'seven years.' I'm sure to some people it sounds amazing but to us it's like, seven years of playing the same person? And this is a tough job, you know?" she said at the British Film Institute and Radio Times Festival.
"It's long, a good nine-mouther. And that's a lot of your life that you sign over to it. I'm going to miss it terribly. But I just can't wait to see where it goes, I just can't wait."
Claire has since handed her crown over to Olivia Colman, for the simple reason that at 33-years-old she's too young to convincingly play the Queen into the 1970s -- where the hit show will venture in its third season.
The actress, though, is thrilled with her replacement, telling reporters recently: "I know who's doing it and I'm not telling you. It's really exciting and great and amazing."
But fans needn't fret!
Claire's next on-screen role will be alongside Ryan Gosling, who plays Neil Armstrong in their upcoming film First Man, directed by Damien Chazelle.
She's also set to take over from Rooney Mara as Lisbeth Salander in the Girl with the Dragon Tattoo series, starring in the upcoming The Girl in the Spider's Web -- her first blockbuster role to date.