Originally placed in genus Zonotrichia (2). Moved to genus Peucaea, then to Aimophila (41, 25), and again restored to Peucaea (42). Both P. cassinii and Botteri's Sparrow (P. botterii) were in the past considered subspecies of Bachman's Sparrow (P. aestivalis). Range overlap, distinctive Flight Song, and nocturnal singing of Cassin's Sparrow were some of the reasons for recognition of both as separate species (43).
No geographic variation has been described, but individuals vary, in fresh plumage, in the extent of reddish versus grayish tone to the dorsum.
No subspecies of Peucaea cassinii (Woodhouse, 1852) have been described.
Among the passerines with 9 primaries (see 44), the Emberizidae (Old World buntings and New World sparrows and seedeaters) is closely related to the Cardinalidae (New World grosbeaks and buntings), Thraupidae (tanagers), and Icteridae (New World blackbirds and orioles). Within the Emberizidae, the sparrows and towhees form a distinct clade (45, 46, 47), of which genus Aimophila sensu lato is a key component. Aimophila and closely related genera constitute a diverse—even in terms of proteins (48)—assemblage of grassland, thorn-scrub, and pine–oak sparrows whose diversity peaks in the southern half of Mexico (3).
Although long treated as a heterogeneous genus, various researchers had acknowledged that Aimophila formed an unnatural clade (e.g., 49). An analysis of sequence variation of 2 mitochondrial genes (50) implied that Wolf’s (3) taxonomy was nearer to a correct reflection of generic limits, although only the 3 species in the ruficeps group were sufficiently distinct from the others to warrant a taxonomic change. Consequently, the American Ornithologists’ Union retained these 3 species—A. ruficeps (the Rufous-crowned Sparrow of western North America), A. rufescens (the Rusty Sparrow of Mexico and northern Central America), and A. notosticta (the Oaxaca Sparrow, endemic to central Oaxaca)—in a restricted Aimophila and transferred all other species into Peucaea (42). The stricter Peucaea recognized by Storer (51) and Wolf (3) did form a clade but one distinct from one of various other species, including several endemic to Mexico (50). This general pattern was supported subsequently by a comprehensive genetic analysis (47), which found that Aimophila sensu stricto and Peucaea are not close phylogenetically. Peucaea is instead sister to a clade of the Arremonops sparrows—a largely tropical radiation, although A. rufivirgatus, the Olive Sparrow, occurs north to southern Texas—and the Ammodramus savannarum (Grasshopper Sparrow) complex, which includes 2 South American species as well, but not other Ammodramus from temperate North America (47).
Within Peucaea, it has long been recognized (e.g., 25, 51, 3) that P. cassinii forms a clade with P. aestivalis (Bachman’s Sparrow of the southeastern United States) and P. botterii (Botteri’s Sparrow of the southwestern-most United States and northern Middle America). All genetic analyses to date have supported this clade, and also that P. cassinii is sister to P. aestivalis (50, 47).