Half the world's populations of Ashy storm-petrels breed in small rock crevices on South Farallon Islands. They are nocturnal, spending their time feeding very far from land.  They use their sense of smell to guide them to their prey.  Ashy storm-petrel is a candidate species for listing  under the Endangered Species Act.

Brandt's cormorant is the most abundant cormorant species on the Farallon islands and the breeding colony on the refuge is one of the largest in the world.  Adults do not leave their nests and young unattended because Western Gulls would steal their eggs and chicks. The feathers of cormorants lack the waterproof characteristics of many waterbird species, and they require land to preen and dry their feathers.

Cassin's Auklet is nocturnal at the nesting colony and makes its nest in soil burrows and rock crevices.  After the first five to six days of hatching, the chick is often left alone in the burrow.  This species is a California Species of Special Concern and is designated by the Fish and Wildlife Service as a Bird of Conservation Concern.

Common Murre is the most abundant breeding seabird in northern and central California.  They nest in very dense colonies on slopes and cliffs.  This species can dive to depths of 100 feet and stay under water for more than one minute.  The deepest dive recorded for the Common Murre was 550 feet.  Murres incubate their one egg with their feet holding the egg in place.

The bright red legs and feed of the Pigeon Guillemot often distinguishes itself from the other seabirds on the Farallon islands.  It utilizes large rock crevices among the talus slopes and cliffs for its nesting site.  They excavate the burrow using their claws and feet.  

Also known as the horn-billed puffin, the Rhinoceros Auklet was extirpated from California around 1860.  Over the last 30-40 years, the Rhinoceros Auklet as expanded to its historic range.  It did not return to the Farallon Islands until 1972 when rabbits were eradicated.  It will spend its time out at sea during the day and return to the nest site only at night.  rhinoceros auklets nest in soil burrows and rock crevices that often faces the ocean.

The Farallon Islands lies at the southern extreme of the Tufted Puffin breeding range.   It is estimated that there are approximately 60 to 100 breeding individuals on the refuge.  It is difficult to access the population because of the inaccessibility of their nesting crevices.  They prefer steep slopes and high elevations for easy takeoff from the nesting site.

The largest single colony of western gulls reside in Southeast Farallon Island.  Its population is on the rise mostly likely due to food availability from garbage dumps.  It is common for western gulls to nest with other seabirds.  During periods of hot weather, western gulls will soak their bellies to cool its eggs during incubation.