The federally endangered Mission Blue, San Bruno Elfin and Callippe Silverspot butterflies all live on San Bruno Mountain. A fourth butterfly, the Bay Checkerspot, was extirpated from the mountain by a fire in 1982 but reintroduced in 2017; it is a federally threatened species. Overall, there are over 30 butterflies native to the mountain.

Birds continue to move freely over and around the mountains and because they offer a large natural respite many of them migrate through or over-winter here. Rare Eastern migrants to visit here include Indigo and Painted Bunting, Gray Catbird, Yellow-shafted Northern Flicker, Tropical Kingbird, Northern Parula, Rose-breasted Grosbeak, White-throated Sparrow, Scarlet Tanager, and nine warblers—Black and White, Black-throated Blue, Blue-winged, Chestnut-sided, Lucy’s, Magnolia, Palm, Prothonotory, and Tennessee.

Other species living on the mountain include Brush and Jack Rabbit, Pocket Gopher, CA Ground Squirrel, Meadow Vole, Deer-Harvest-House and Parasitic Mouse, Feral House Cat, Gray Fox, Long-tailed Weasel, Raccoon, Striped Skunk, Trowbridge’s Shrew and Opossum, there have been sightings or confirmed populations of the Mountain Lion, Red Fox, Coyote, Black-tailed Deer, Badger, Bobcat, Eastern Fox Squirrel and Western Gray Squirrel.