Given the abundance of elephants seals on Southeast Farallon Island, it is hard to believe that they were once hunted to extirpation in the 19th century.  Elephant seals recolonized the refuge in 1959 and now breed and give birth on the refuge.

Northern fur seals was once the most abundant pinniped on the Farallon Islands at the time of human arrival with breeding colonies numbering in the tens of thousands.  They were also hunted to extirpation in the 1800s.  In 1996, the first fur seal pup was recorded on the refuge.  Since then, births have increased slowly.

California sea lions haul out year-round onto the refuge and are the dominant species on the refuge.  These fast and agile swimmers take advantage of the abundant food source around the Farallon Islands and in turn, are one of the primary food sources of white sharks.

Harbor seals tend to haul out onto the Farallon Islands.  They are the least vocal of the pinnipeds listed here although males will roar underwater to attract mates.  Pups can swim a few hours after birth.

Stellar sea lions are the largest of all sea lions.  They were listed as endangered in 1990 when 50 percent of its population declined from 1960s to 1989.  Possible reasons for the decline include pollution, human disturbance, overfishing, increased disease and/or predation, and El Niño effects.