Commission members voted Wednesday to replace Dan Richards.
Richards, who was appointed by Gov. Arnold Schwarzenegger in 2008, has said he plans to remain on the five-member commission until his term expires in six months.
Richards was criticized by animal welfare groups after a photo of him with the dead mountain lion surfaced.
Hunting mountain lions is banned in California, though it's legal in Idaho and other states.
Richards has said he did nothing wrong. He has been defended by hunting groups.
The commission's new president is Jim Kellogg of Discovery Bay.