In the southern Appalachians, males have the crown and dorsum streaked black, and females are darker ( Ridgway, R. (1902). The birds of North and Middle America, Pt. 2. U.S. Natl. Mus. Bull. no. 50. Close Ridgway 1902) relative to birds that breed farther north. Colorimetry data of first-year and second-year males indicate that southern (North Carolina) birds are measurably darker than northern (Pennsylvania) birds ( Graves, G. R. (1997a). Age determination of free-living male Black-throated Blue Warblers during the breeding season. J. Field Ornithol. no. 68:443-449. Close Graves 1997a). These populations exhibit limited but statistically significant differentiation in the control region of the mitochondrion, and molecular analyses indicate rapid expansion from a single glacial refugium since the late Pleistocene ( Davis, L. A., E. H. Roalson, K. L. Cornell, K. D. McClanahan and M. S. Webster. (2006). Genetic divergence and migration patterns in a North American passerine bird: Implications for evolution and conservation. Molecular Ecology no. 15 (8):2141-2152. Close Davis et al. 2006, Grus, W. E., G. R. Graves and T. C. Glenn. (2009). Geographic variation in the mitochondrial control region of Black-throated Blue Warblers (Dendroica caerulescens). Auk no. 126 (1):198-210. Close Grus et al. 2009).

Two subspecies ( Ridgway, R. (1902). The birds of North and Middle America, Pt. 2. U.S. Natl. Mus. Bull. no. 50. Close Ridgway 1902, American Ornithologists' Union. (1957). Check-list of North American birds, 5th ed. Washington, D.C: Am. Ornithol. Union. Close American Ornithologists' Union 1957), diagnosed on the basis plumage shade (blacker or darker vs. bluer or paler). The validity of southern subspecies was questioned ( Dwight, J., Jr. (1900). The sequence of plumages and moults of the passerine birds of New York. Annals of the New York Academy of Sciences 13:73-360. Close Dwight 1900c), and differences are slight, with some evidence of clinal variation ( Grus, W. E., G. R. Graves and T. C. Glenn. (2009). Geographic variation in the mitochondrial control region of Black-throated Blue Warblers (Dendroica caerulescens). Auk no. 126 (1):198-210. Close Grus et al. 2009). Overwintering ranges of the subspecies are effectively unknown, but stable isotopes of hydrogen and carbon suggest that northern breeders overwinter chiefly on Cuba and Jamaica, whereas southern breeders overwinter chiefly on Hispaniola and Puerto Rico ( Rubenstein, D. R., C. P. Chamberlain, R. T. Holmes, M. P. Ayres, J. R. Waldbauer, G. R. Graves and N. C. Tuross. (2002). Linking breeding and wintering ranges of a Neotropical migrant songbird using table isotopes. Science no. 295:591-593. Close Rubenstein et al. 2002). If direct evidence from specimens collected in overwintering range supports this west–east split, then either the type locality of the nominate subspecies needs to be redesignated (ideally to a breeding site), or the nominate applies to the southern populations and the northern becomes Setophaga c. leucoptera ( Wilson, A. (1812). American ornithology. Vol. 5. Philadelphia, PA: Bradsford and Inskeep. Close Wilson 1812), with a presumed type locality of Pennsylvania.

S. c. caerulescens (Gmelin, 1789). Includes Sylvia leucoptera Wilson, 1812; S. palustris Stephens, 1817; S. macropus Vieillot, 1823; S. sphagnosa Bonaparte, 1824; and Syvicola pannosa Goose, 1847. Breeds from southeastern Canada (southern Ontario east to the Maritimes) south into the northern United States from Minnesota east to Pennsylvania; overwinters in the Greater Antilles and adjacent islands [type locality = Hispaniola]. Male with the dorsum deep steel-blue, the crown paler than the mantle; female olive dorsally and washed dull yellow ventrally.

S. c. cairnsi (Coues, 1897). Breeds in the Appalachians from southwestern Pennsylvania and West Virginia south to northern Georgia [type locality = western North Carolina]; overwinters in the Greater Antilles. Like S. c. caerulescens, but the male has the crown darker blue and concolorous with a mantle typically blotched with some black and the female is darker and duller olive with the ventrum less yellow.

The American wood-warblers (Parulidae) are a key component in a broad and geologically recent radiation of passerines with 9 primaries that also includes the families Emberizidae, Cardinalidae, Thraupidae, and Icteridae ( Klicka, J., K. Burns and G. M. Spellman. (2007). Defining a monophyletic Cardinalini: A molecular perspective. Molecular Phylogenetics and Evolution 45:1014-1032. Close Klicka et al. 2007). Within the Parulidae, a comprehensive genetic study ( Lovette, I. J., J. L. Perez-Eman, J. P. Sullivan, R. C. Banks, I. Fiorentino, S. Cordoba-Cordoba, M. Echeverry-Galvis, F. K. Barker, K. J. Burns, J. Klicka, S. M. Lanyon and E. Bermingham. (2010). A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves). Molecular Phylogenetics and Evolution no. 57 (2):753-770. Close Lovette et al. 2010) shook up generic relationships. A key finding was that the genus Dendroica was paraphyletic with Wilsonia citrina (the Hooded Warbler) and Setophaga ruticilla (the American Redstart). As a result, all species of Dendroica warblers, as well as W. citrina, were merged into the genus Setophaga ( Chesser, R. T., R. C. Banks, F. K. Barker, C. Cicero, J. L. Dunn, A. W. Kratter, I. J. Lovette, P. C. Rasmussen, J. V. Remsen Jr., J. D. Rising, D. F. Stotz and K. Winker. (2011). Fifty-second supplement to the American Ornithologists' Union Check-list of North American Birds. Auk no. 128 (3):600-613. Close Chesser et al. 2011), the oldest name and a genus that for many decades was thought to be monotypic. Hence, Setophaga went from being monotypic to the most speciose genus (34 species) in the family, easily surpassing the Neotropical genus Basileuterus (26 species).

Setophaga caerulescens has no close relative but is instead basal to a broad radiation of congeners ( Lovette, I. J., J. L. Perez-Eman, J. P. Sullivan, R. C. Banks, I. Fiorentino, S. Cordoba-Cordoba, M. Echeverry-Galvis, F. K. Barker, K. J. Burns, J. Klicka, S. M. Lanyon and E. Bermingham. (2010). A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves). Molecular Phylogenetics and Evolution no. 57 (2):753-770. Close Lovette et al. 2010); as such, it is not sister to S. cerulea (the Cerulean Warbler), contra Mayr, E. and L. L. Short. (1970). Species taxa of North American birds, a contribution to comparative systematics. Vol. 9: Publications of the Nuttall Ornithological Club. Close Mayr and Short 1970. The only potential hybrid involving the species is a cross with S. petechia, the Yellow Warbler, reported from Quebec ( Ducharme, C. and J. Lamontagne. (1992). Un cas d'hybridation chez les parulines? Dendroica caerulescens x Dendroica petechia. Québec Oiseaux no. 4:1-6. Close Ducharme and Lamontagne 1992).