Tanya McVeigh Peterson, a member of the zoo society board, has been appointed interim director, according to zoo spokeswoman Gwendolyn Tornatore.
Mollinedo has served as the zoo's director and president since 2004 and previously served as director of the Los Angeles Zoo for eight years, Tornatore said.
Mollinedo's resignation comes nearly six months after a tiger escaped from its enclosure on Christmas Day and killed 17-year-old Carlos Sousa Jr. and injured his friends, 19-year-old Amritpal and 23-year-old Kulbir Dhaliwal.
Mollinedo and his wife, Marilyn, intend to retire in the Bay Area, Tornatore said.