Arctocephalus pusillus has two sub-species, A. p. pusillus and A. p. doriferus, which are separated by the ocean between Africa and Australia. Skull characteristics of the two subspecies are similar enough to place them in one species. A notable difference between the two is the crest between the mastoid process and the jugular process of the exoccipital, which is proportionately larger in A. p. pusillus (King, 1983).

Males of the South African or cape fur seal subspecies, A. p. pusillus, are an average of 2.3 meters in length and weigh from 200 to 350 kg (King 1983). Their coat is gray or black in color and is lighter on the underside (King 1983, Schliemann 1990). Female African fur seals are smaller, weighing an average of 120 kg (King 1983) and measuring an average of 1.8 meters long (Schliemann 1990). Their coats are brown with lighter shading on the underside.

Males of the subspecies A. p. doriferus, the Australian fur seal, weigh anywhere from 218-360 kg and are 2-2.2 meters in length (King 1983). Their coats are a gray-brown and they have a thick mane about their neck region which is slightly lighter (King, 1983). Female Australian fur seals vary greatly in size, weighing between 36 and 110 kg and measuring between 1.2 and 1.8m in length (King 1983, Schliemann 1990). Their coat is a silver-gray with a yellow colored throat and brown underside. (King, 1983; Schliemann, 1990)