The rhinoceros auklet (Cerorhinca monocerata) has sometimes been included in the genus Fratercula, and some authors place the tufted puffin in the genus Lunda. The puffins and the rhinoceros auklet are closely related, together composing the subfamily Fraterculini.
The scientific name Fratercula is derived from Latin and means "little brother", a reference to the black and white plumage, which resembles monastic robes.
The English name "puffin" – puffed in the sense of swollen – was originally applied to the fatty, salted meat of young birds of the unrelated Manx shearwater (Puffinus puffinus), formerly known as the "Manks puffin". Puffin is an Anglo-Norman word (Middle English pophyn or poffin) for the cured carcasses of nestling Manx shearwaters.
The oldest alcid fossil is Hydrotherikornis from Oregon dating to the Late Eocene while fossils of Aethia and Uria go back to the Late Miocene. Molecular clocks have been used to suggest an origin in the Pacific in the Paleocene. Fossils from North Carolina were originally thought to have been of two Fratercula species, but were later reassigned to one Fratercula, the tufted puffin, and a Cerorhinca species. Another extinct species, Dow's puffin (Fratercula dowi) was found on the Channel Islands of California until the Late Pleistocene or early Holocene.
The Fraterculini are thought to have originated in the Pacific primarily because of their greater diversity there; there is only one extant species in the Atlantic, compared to two in the Pacific. The Fraterculini fossil record in the Pacific extends at least as far back as the middle Miocene, with three fossil species of Cerorhinca, and material tentatively referred to that genus, in the middle Miocene to late Pliocene of southern California and northern Mexico. Although there no records from the Miocene in the Atlantic, a re-examination of the North Carolina material indicated that the diversity of puffins in the early Pliocene was as great in the Atlantic as it is in the Pacific today. This diversity was achieved through influxes of puffins from the Pacific; the later loss of species was due to major oceanographic changes in the late Pliocene due to closure of the Panamanian Seaway and the onset of severe glacial cycles in the North Atlantic.