The former Live from Studio Five presenter and Roberts wed in Bali in 1998.
Messenger's agent said that the pair are determined to remain friends for the sake of their three children Morgan, 12, Flynn, 10, and Evie, 8.
They said: "[Messenger and Roberts] are now separated after a very long time. It's one of those things.
"They are very good friends, and all that matters is the children, and they will make sure they are well looked after. It's very amicable."
The couple had previously undergone a trial separation, which lasted eight months, in 2008.
Messenger said in April that her and Roberts's relationship suffered from arguments.
She said: "We've been working through a lot. We had some terrible rows."