Adult males in the western part of this species' breeding range—west of the Ozark

No subspecies (Storer 1951, Thompson 1991b). Traditionally, two subspecies have been recognized (Am. Ornithol. Union 1957, Paynter 1970): the paler, smaller P. c. pallidior (Mearns, 1911) in the West and the darker, larger P. c. ciris (Linneaus, 1758) in the East. Nevertheless, subspecies differences are weak (Storer 1951), with plumage color and size overlapping considerably and varying in a smoothly clinal manner (Thompson 1991b). The clinal nature of variation is emphasized by the uncertain placement of the boundary between named subspecies, as some have argued that phenotypic turnover occurs farther east than 96°W longitude (Storer 1951, Robbins and Easterla 1992). In any case, the dividing line between taxa does not coincide with the well documented 550-km gap at 85°W that separates breeding populations in the s.-central U.S. from those on the se. Atlantic coast. It is doubtless true that gene flow between populations on either side of this gap is more limited than between the putative subspecies (Thompson 1991b), a notion that led Sibley and Monroe (1993) to the radical conclusion that the gap divides two Painted Bunting species. Recent genetic data show separation between Atlantic coast and interior populations rather than between the supposed subspecies (Herr et al. 2011).

The genus Passerina, which comprises 7 species confined to North America, has traditionally been placed in the family Cardinalidae, or in the tribe Cardinalini if a broad family of Emberizidae is recognized. A recent comprehensive molecular phylogeny (Klicka et al. 2007) placed the genus sister to a clade containing the Cyanocompsa buntings and grosbeaks of the Neotropics, and Passerina is also near the tropical genera Cyanoloxia and Porphyrospiza (Sibley and Monroe 1990, Tamplin et al. 1993). Passerina is an old genus: Steadman and McKitrick (1982) referred to the genus' three incomplete humeri that were approximately 4 million years old and intermediate in size between P. amoena (the Lazuli Bunting) and P. caerulea (the Blue Grosbeak).

Within the genus Passerina, the nearest extant relative of P. ciris appears to be P. versicolor, the Varied Bunting of the sw. United States and nw. Mexico (Klicka et al. 2001). Hybridization in the wild involving P. ciris is rare, but the species has crossed with its sister species (Storer 1961) and with P. cyanea, the Indigo Bunting (Taylor 1974). Additional hybrids are known from captivity (Thomasset 1915, Pyle 1997).