Migratory birds find their way to the Farallon Islands during the migration season. More than 400 species have been recorded. In addition to birds like burrowing owls, warblers, and nuthatches, the researchers living on the refuge occasionally see accidental migrants like the northern gannet. Birds, marine mammals, and plants are not the only wildlife that occurs on the islands. An arboreal salamander (that interestingly does not live in trees on the Farallons), crickets, beetles, and other invertebrates are year-round residents. The island is visited by traveling butterflies, dragonflies, and bats. Studies of the transient bats are in the early stages. Non-native house mice are also found on the island, to the detriment of nesting birds and native plants. White sharks are found in the waters around the island, feeding on seals and sea lions. Research identifying individual by scars and markings along with a project using satellite relay tags is helping scientists better understand white sharks. Evidence analyzed by PRBO Conservation Science revealed that many sharks that had been tagged at the Farallons appear to head to Hawaii after leaving the Farallons. They then travel to the southern coast of Mexico before returning to the island. Farallon Refuge is truly a unique and diverse ecological community.
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Farallon National Wildlife Refuge is managed as part of the San Francisco Bay National Wildlife Refuge Complex.