Pinnipeds are seals, sea lions, and walruses. Some scientists classify Pinnipedia as a suborder of Order Carnivora.

Phocidae includes all "true" seals. True seals lack external ear flaps; have a stout, round body; and are unable to rotate their hind flippers forward.

Most scientists recognize five subspecies of harbor seals: P.v. richardsi, P.v.vitulina, P.v. concolor, P.v. mellonae, and P.v. stejnegeri. Each subspecies is separated geographically, and so is reproductively isolated. Historically, scientists classified P. largha (the largha seal) as a harbor seal subspecies. Currently, P. largha is widely recognized as a separate species. The harbor seal also is known as the common seal.

The earliest phocid fossils date back 12 to 15 million years.

Ancestral phocids gave rise to modern harbor seals, which appeared in the North Pacific two to three million years ago when the Bering Strait formed.

The skeleton and limb structure of pinnipeds shows that the ancestors of harbor seals once were able to walk on land. Scientists, however, have not found fossil evidence to identify a common ancestor with living land mammals.