Two subspecies of Passerina leclancherii usually are recognized:
leclancherii, described by Lafresnaye 1840; type locality Acapulco, Guerrero, Mexico.
This subspecies is restricted to the coastal areas of central Guerrero, Mexico, near El Limon, Coyuca, and Acapulco (Friedmann et al. 1957).
grandior, described by Griscom 1934; type locality Chivela, Oaxaca, Mexico.
Occurs thoughout the Pacific coast from Nayarit to northwestern Chiapas, excepting that of Guerrero, and in the lower interior valleys of Mexico (Miller et al. 1957). It is identical to leclancherii except significantly larger (Griscom 1934); see Measurements.
Klicka et al. used phylogenetic analysis of mitochondrial DNA sequence data (from the cytochrome-b gene) to resolve relationships within Passerina. This study divided into two clades, including a "painted" clade composed of P. rositae (Rose-bellied Bunting), P. leclancherii (Orange-breasted Bunting), P. ciris (Painted Bunting), and P. versicolor (Varied Bunting). Within this clade, leclancherii was sister to the pair ciris and versicolor, while rositae was sister to the entire painted clade. The "painted" clade is united by plumage patterns, including some blue plumage, bright carotenoid pigments (yellow, pink, or scarlet), and a conspicuous eye ring. This clade has short internode distances, suggesting that such coloration traits would accelerate divergence (Klicka et al. 2001). This study also designed a molecular clock using fossils discovered in Mexico and two different divergence rates (2% and 1.6%), finding that the genera Passerina and Cyanocompsa probably diverged between 4.1 and 7.3 million years ago, during the Late Miocene, rejecting previous ideas that this occurred in the Late Pleistocene (Klicka et al. 2001).
One possible hybrid was collected after it struck a window in Toluca, Mexico (Sanchez 2005). This bird was a male with abundant fat reserves and unusual plumage, with a blue head similar to Passerina ciris and a yellow breast with an orange breast band similar to leclancherii. The collectors suggested it was a hybrid but did not address the possibility of it being an escaped bird (Sanchez 2005).
An analysis of different color properties of the plumages of cardinalid bunting in tetrahedral color spaces (Stoddard and Prum 2008) determined that leclancherii had some of the highest reflective properties in the belly, the highest chroma values (distance from a colorless point in the tetrahedral space, the achromatic point). Its crown and breast colors were also particularly simulative to its color cones. Overall, the ‘painted’ clade (or at least two members of it, usually Orange-breasted and Painted Buntings) had some of the largest color diversities, hue disparities (caused by the contrast of blue and a carotenoid color), high color span (overall color contrast), high chromas, and the highest color spans (distances between colors). However, there was no relationship found between the evolution of color and the birds’ phylogenies. Rather, they more likely evolved due to accelerating rates of change in each individual species. However, if analyzed through the whole family, the consistent presence of blue coloration would probably prove to be a phylogenetic trait (Stoddard and Prum 2008).
This genus is embedded in the Cardinalidae, which was recently re-defined within the nine-primaried oscines (Klicka et al. 2007). Although data suggested that this family is closest to Thraupidae and sister to an Emberizidae-Icteridae-Parulidae clade, this tree was not well supported due to insufficient sampling. However, the family Cardinalidae is strongly supported and consisted of five clades: a ‘masked’ clade (genera Cardinalis, Caryothraustes, Peripophyrus, Rhodothraupis, and Piranga), the Habia and Chlorothraupis (those genera), the Pheucticus (that genus), the Granatellus (that genus), and a ‘blue’ clade (genera Cyanocompsa, Amaurospiza, Cyanoloxia, Passerina, and Spiza). Within the ‘blue’ clade, the Cyanocompsa-Cyanoloxia-Amaurospiza clade is sister to the Passerina, and Spiza is sister to both (Klicka et al. 2007).