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. The magnificent Pipevine Swallowtail is found only in Firth Canyon in southern Brisbane and a couple miles northwest in lower Colma Canyon. Nothing overwhelms the senses more than to be standing on a ridge top during a full-blown migration of Painted Ladies.

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. Because the mountains lie between the bay and the ocean many local transients pass over or briefly land as they commute.

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.