Morel made his debut for FC Lorient at the age of 19, as a substitute for Pape Malick Diop in Lorient's 1–0 defeat at home to FC Gueugnon on 19 April 2003. He played in only one further match that season due to a snapped banjo, but has progressively played a larger part in Lorient's lineup.
In Lorient's 2005–06 promotion season, he played in 29 matches.
On 19 June 2011, Morel left Lorient to join league rival Olympique Marseille, signing a contract lasting until 30 June 2015. He had a nine-year spell with his hometown club.