"After five years of presidency Pape Diouf will leave his job. I want to congratulate him for his work at the club," Robert Louis-Dreyfus said in a statement without making clear whether he had been sacked or was quitting.
"He has been a great chairman who has done everything for Olympique Marseille. From a sporting point of view he lifted the club to the highest level in France."
"Unfortunately some differences of opinion have appeared and we cannot go on together," Louis-Dreyfus added.
"We have new challenges ahead of us. A new chairman will be named in the coming days."
Diouf had been in conflict with the club's supervisory board director Vincent Labrune, who is also Louis-Dreyfus's spokesman.
The chairman did not show up at a supervisory board meeting last week after being summoned, saying he was celebrating Marseille's under-16 title.
Diouf had gained support from the club's eight fan groups, who organised a petition to save his job.
