The Avengers has reportedly been keeping her separation under wraps for some time.
A source told People: “They’ve been separated since the summer.”
Rumours were first sparked that they had gone their separate ways when the mum of one was spotted without her wedding ring at the Women’s March protest against President Trump.
She was last pictured wearing her ring in December.
The Lost In Translation star married the French advertising agency owner in 2014.
They apparently met through mutual friend, tattoo artist Fuzi Uvtpk in 2012, getting engaged 10 months later.
Their daughter Rose was born in 2014 and they married shortly after.
A source said to E! that their wedding day was a relaxed affair.
“They were really laid back and friendly and almost always had the baby,” they said.
“They were holding hands and hugging and smiling and flirting with each other. You could tell they were really happy.”
Scarlett was previously married to actor Ryan Reynolds but they divorced in 2011 after three years of marriage.
The 32 year old has also dated actor Sean Penn.
After entering a relationship with Romain, Scarlett said she didn’t want to tie the knot again.
“I never think about marriage,” she said. “It’s really not important to me. It has no relevance to me right now.”
“I’m in a nice relationship, I’m working a lot.
“To me, being in a functioning relationship doesn’t mean you have to be married.”
Scarlett recently revealed that she was attempting to learn her husband’s native language of French.
“When you’re in a relationship with somebody you want to speak whatever language is easiest to get your ideas out as quickly as possible, so you can argue your point,” she said.