Body size and the color and size of crest (in breeding plumage) vary considerably across the species' breeding range. Size tends to increase with latitude (Palmer 1962), fitting the expected pattern of Bergmann's rule. Alaskan birds are largest and have the crest long, straight and mostly white. Birds from e. North America are smaller and have the crest short, curled, and black. The smallest individuals are from the Bahamas. Distribution of crest characters is poorly known, in part because crests are present only briefly, early in the breeding season. The color of bare skin of the lores and gular vary seasonally and deserve attention (see Appearance, below). Characteristics of birds that breed in Mexico have not been examined comprehensively. Mitochondrial and microsatellite data provide evidence that Alaskan breeders may diverge genetically from other populations in North America (Mercer et al. 2013). A divergent lineage may be present in the southwestern portion of the species' range (i.e., s. California and nw. Mexico), although further study is needed (Mercer et al. 2013), and additional data are needed for the n. Atlantic population (Waits et al. 2003, Green at al. 2006, Fyke et al. 2010, Mercer et al. 2013). Studies from regions of overlap have not examined whether assortative mating occurs. Banding recoveries suggest little mixing across the Rocky Mts. (Dolbeer 1991).
Five subspecies, following Dorst and Mougin (1979) and Watson et al. (1991), differentiated by body size (see Measurements, below), overall color saturation, and color and shape of the crest during the breeding season.
P. a. cincinatus (Brandt, 1837). Breeds in Alaska, winters south to British Columbia [type locality = Kodiak I., Alaska]. Crest white and straight; body size large (male wing > 310 mm, male weight > 2000 g).
P. a. albociliatus Ridgway, 1884. Breeds along the Pacific Coast from British Columbia to Baja California and Sinaloa, and inland, possibly as far east as New Mexico, Utah, and Montana [type locality = Pacific Coast of California]. Like P. a. cincinatus, but crest variably mixed white and black; averages smaller (male wing < 320 mm).
P. a. auritus (Lesson, 1831). Supercedes Hydrocorax dilophus Vieillot, 1817. Breeds over most of range in e. and central North America; largely migratory, wintering from mid-Atlantic Coast to Gulf of Mexico [type locality = Saskatchewan R., e. Canada]. Similar to P. a. albociliatus, but crest black and curled (Figure 2); size variable but in general between that of P. a. cincinatus and P. a. albociliatus (Appendix 3).
P. a. floridanus (Audubon, 1835). Resident in Florida and Caribbean [type locality = s. Florida]. Like P. a. auritus, but smaller (male wing 280–310 mm, male weight generally 1300–2000 g).
P. a. heuretus Watson, Olson, and Miller, 1991. Endemic to San Salvador in the Bahamas, although it may occur on other islands of the Bahamas (Watson et al. 1991) and on Cuba (Garrido and Kirkconnell 1992). Like P. a. floridanus, but small (male wing < 280 mm, male body mass < 1300 g), being much the smallest subspecies, to the point that it overlaps broadly in size with P. brasilianus, the Neotropic Cormorant (Watson et al. 1991).
Monophyly of the Pelecaniformes has been disputed for decades (Cracraft 1985, Hedges and Sibley 1994, Siegel-Causey 1997), with modern molecular surveys (e.g., Hackett et al. 2008) tending to support arguments that the order is paraphyletic. In all studies, however, the Sulidae (boobies and gannets) groups consistently with the Phalacrocoracidae (cormorants), Anhingidae (darters), and Fregatidae (frigatebirds), the other families in the so-called “core Pelecaniformes,” a misnomer because family Pelecanidae (pelicans) is nearer to Ardeidae (herons and egrets). Hence, the core groups are now placed in the order Suliformes.
The genus Phalacrocorax is comprised of the typical cormorants, although there appears to be enough of a division within the genus that it may need to be subdivided to reflect accurately among-species relationships (van Tets 1976, Siegel-Causey 1988). Regardless, both morphology (Siegel-Causey 1988) and genetics (Kennedy et al. 2000, 2009) support a hypothesis that P. auritus is sister to P. brasilianus. These two even have been treated as allospecies of a superspecies (see Sibley and Monroe 1990).