The shock announcement comes one year after they welcomed their second daughter, Marnie Mae Ellis, a little sister for their four-year-old Florence.
Confirming the news to the Mail, a representative said the couple will "remain friends".
A statement read, "Tamzin Outhwaite and Tom Ellis are sad to confirm they have separated. They continue to support each other as parents and will remain friends. They ask for sensitivity at this difficult time."
Tamzin, 42, and Miranda actor Tom, 34, were married in June 2006. The couple, who both starred in EastEnders, tied the knot a year after meeting through their mutual friend James McAvoy.
It was only in March of this year that Tom spoke lovingly about the moment he met his future wife.
"My life changed in 2005 on the day I met my wife, Tamzin Outhwaite," he wrote on the Mail website.
"She was in a play called Breathing Corpses with James McAvoy, one of my best mates from drama school. I knew who she was and I’d fancied her quite a bit when she played Melanie Owen in EastEnders."
After spotting her in a bar a few days later, Tom revealed that they "chatted together for the rest of the night."
"I gave her a lift home and told her I'd love to see her the next day… After just a couple of weeks, I already knew she was the person I wanted to spend the rest of my life with."
Tom, who has a daughter Nora from a previous relationship, has been busy shooting his lead role in ABC pilot Gothica, a modern day supernatural thriller.
Tamzin, meanwhile, will next appear on screen in BBC drama New Tricks, taking over the starring female role from Amanda Redman.