Reasons for why Patrick S. Larkin decided to step down effective Friday have not been released, said Pauline Nash, Rancho Santa Ana Botanic Garden spokeswoman.
Board of Trustees member Elin R. Dowd said the garden appreciated the leadership Larkin gave the organization.
"Rancho Santa Ana Botanic Garden experienced considerable growth during Mr. Larkin's tenure," Dowd said.
"He has left RSABG in a good position to continue to promote the conservation and appreciation of California native plants."
The garden at 1500 N. College Ave. is dedicated to California native plants and environmental conservation.
Trustees have appointed Lucinda McDade, the garden's Judith B. Friend director of research, to serve as interim director.
Larkin joined the garden in 2004 as an interim director and was appointed to be executive director in 2005.
During Larkin's tenure, the garden's non-endowment revenue and membership tripled.
However, a Facebook page titled "What is the future of Rancho Santa Ana Botanic Garden?" criticized Larkin in June 2010 after seven staffers were laid off because of budget cuts. One poster wrote "This cannot be good for the mission of the garden! ... Please don't let them get away with making the historically important Rancho Santa Ana Botanic Garden into just another pretty park."
Officials said the garden's endowment historically accounted for up to 70 percent of the core operating budget, but it lost about 23 percent of its value during the past fiscal year.
"It's not happy, and it's not cheerful," Larkin had said. "The nature of the cuts was such that almost every department was affected."