The pair welcomed their second child just three weeks ago. The couple also have a daughter, Poppy Alice, who is almost two-years-old.
A source close to the pair told The Daily Telegraph that “things have been bad for a while”.
“They tried to keep it together but it all went to s**t, that's the honest truth. It is pretty messy,” the source said.
The source also revealed that the break-up was hard on Phoebe as Sam's mother Julie was standing by her son.
"It would have been hard for Phoebe because Julie would have completely stuck by Sam... and there's talk she didn't offer Phoebe much support," the source added.
The Daily Mail published photos of the rugby star arriving at the couples home on Wednesday and leaving shortly after with numerous overnight bags.
Phoebe's mother was then snapped arriving at the house with a large suitcase.
In September Sam found himself at the centre of a video chat scandal after his Facebook account was reportedly used to send nude photos to a 23-year-old woman.
He was later cleared of any wrongdoing.
“I’m not angry. What hurts me the most is seeing my wife upset about what’s out there,” the father of two told reporters during a press conference at the Rabbitohs’ Redfern training headquarters.