The following is a list of endangered and threatened species in San Francisco and it's surrounding waters.
- White Abalone
- Mission Blue Butterfly
- San Bruno Elfin Butterfly
- Tidewater Goby
- Coho Salmon
- Central California Coastal Steelhead
- Chinook Salmon
- California Red-Legged Frog
- Loggerhead Turtle
- Green Turtle
- Leatherback Turtle
- Ridley Sea Turtle
- Western Snowy Plover
- Short-Tailed Albatross
- Bald Eagle
- California Brown Pelican
- California Clapper Rail
- Guadalupe Fur Seal
- Sei Whale
- Blue Whale
- Finback Whale
- Right Whale
- Steller Sealion
- Humpback Whale
- Sperm Whale
- Salt Marsh Harvet Mouse
- Raven's Manzanita
- Presidio Clarkia
- Marin Dwarf-Flax
- San Francisco Lessingia