The Farallon Islands are a barren cluster of rocks about 30 miles west of San Francisco. The largest of the islands, Southeast Farallon Island and West End Island, cover just 110 acres, and have been the focus of important research on breeding seabirds and migratory songbirds for decades. The waters around the islands are managed as the Gulf of the Farallons National Marine Sanctuary (National Oceanic and Atmospheric Administration), and the USFWS owns the islands and manages it as part of the San Francisco Bay National Wildlife Refuge Complex. Ecological research on birds is coordinating jointly by US Fish & Wildlife Service and PRBO Conservation Science.

These islands support an astounding number and diversity of breeding California seabirds, and in 2000, hosted the world's largest breeding colonies of Ashy Storm-Petrel (and some of largest aggregations of breeding Brandt's Cormorant (5800 birds), Western Gull (nearly 10,000 pair), Pigeon Guillemot (800+ pair) and Cassin's Auklet (Abraham et al. 2000).

Population estimates have dramatically changed since 2000, with species both gaining and losing numbers. Brandt's grew from approximately 5,800 birds in 2000 to over 20,000 breeders in 2007 and Common Murres now number close to 250,000, roughly four times the number present in 2000 (Pete Warzybok, via email 2008).

California Gulls colonized the Farallones during 2008. This is the first time this species has been recorded breeding in a wholly marine environment and brings the number of breeding seabird species on the island to 13.

The Farallones are also an important stopover location for many migrant songbirds and a refuge for vagrant species that are lost or blown off course.

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The islands are accessible only to researchers, and in this regard are well protected. However, oil spills at sea and along the current (such as the November 2007 Cosco Busan spill in San Francisco Bay) remain a threat. Half of the ten known oil spills in California since 1985 have occurred around the Farallons (located along a major shipping lane), which have resulted in population-wide impacts at least to Common Murre (Steve Hampton, personal communication). Gill-net fisheries may also pose a threat to breeding seabirds, both by direct impacts to birds (incidental catch) and by reduction of their food source. New regulations as part of the creation of Marine Protected Areas around the islands will help to reduce the likelihood of some fishing-related threats.