The county is home to several endangered species including the San Francisco garter snake and the San Bruno elfin butterfly, both of which are endemic to San Mateo County. The endangered Ridgway's Rail is also found on the shores of San Francisco Bay, in the cities of Belmont and San Mateo. The endangered wildflower Hickman's potentilla is found near the Pacific Ocean on the lower slopes of Montara Mountain. The endangered wildflowers White-rayed pentachaeta, Pentachaeta bellidiflora, San Mateo Woolly Sunflower, Eriophyllum latilobum, Marin Dwarf Flax, Hesperolinon congestum and the San Mateo Thornmint, Acanthomintha duttonii, are found in the vicinity of the Crystal Springs Reservoir.

In May 2014, a California condor was spotted near Pescadero, a coastal community south of San Francisco—it was the first California condor spotted in San Mateo County since 1904. The condor, tagged with the number "597", and also known as "Lupine", is one of 439 condors living in the wild or captivity in California, Baja California and Arizona. The three-year-old female flew more than 100 miles (160 km) north from Pinnacles National Park, in San Benito County, on May 30, and landed on a private, forested property near Pescadero, on the San Mateo County Coast, where it was photographed by a motion-activated wildlife camera. Harold Heath, Professor Emeritus, of Stanford University was responsible for the 1904 sighting, 1 mile (1.6 km) west of the University campus.

Pumas (Puma concolor), also known as cougars or mountain lions, roam the county.

Tule elk (Cervus canadensis nannodes) were native to San Mateo County and among the "favored foods" of the Ohlone people based on ethnohistoric and archeological evidence there. The discovery of two elk specimens made news in 1962, one a royal elk (royal elk bulls have six tines per antler) from a peat bog excavated in Pacifica's historic Laguna Alta, and now in the Museum of Vertebrate Zoology collection. These may date from the time of Spanish settlement. Laguna Alta lay just south of the Interstate 280 and Skyline Boulevard intersection, east of Mussel Rock. The California Academy of Sciences also has an elk skull fragment collected one mile inland from the mouth of Purisima Creek in 1951. Additional coastal elk remains dating from the Middle and Late Periods in Northern California were found in at least five more late Holocene archeological sites in San Mateo County: SMA-115 (Montara State Beach site), SMA-118 (Bean Hollow State Beach site), SMA-244 (Butano Ridge site), SMA-97 (Año Nuevo Creek site) and SMA-218 (Año Nuevo State Reserve site). On the eastern side of the San Francisco Peninsula, elk remains were also unearthed at multiple archaeological sites along San Francisquito Creek.
What are three mammals found within San Mateo County?
Pumas and tule elk are two mammal species found in San Mateo County.