Two subspecies of Bushy-crested Jay generally are recognized (e.g. Hellmayr 1934, Blake and Vaurie 1962):
nominate melanocyanea of Guatemala, southern El Salvador, and Honduras; see Detailed Description.
Cyanocorax melanocyanea chavezi (Miller and Griscom 1925), of Nicaragua (type locality: Matagalpa, Nicaragua) and southern Honduras. "Similar to C. m. melanocyanea, but black areas extending on the upper back and all over the breast; belly and under tail coverts much darker, deep dusky Prussian blue, instead of light grayish glaucous blue; upper parts, especially the back, darker, more cobalt blue" (Hellmayr 1943).
Blake and Vaurie (1962) reported that melanocyanea and chavezi intergrade in northern and eastern El Salvador. Monroe (1968), on the other hand, believed that "the amount of black below is largely dependent upon individual variation within these populations" and so although "there is a tendency towards a greater frequency of black-bellied birds toward the south," Monroe considered the species to be monotypic.
The Bushy-crested Jay and closely related species - San Blas Jay (Cyanocorax sanblasianus), Yucatan Jay (Cyanocorax yucatanicus), and Purplish-backed Jay (Cyanocorax beecheii) - variously have considered to be members of the large genus Cyanocorax (Hardy 1969, Phillips 1986, American Ornithologists' Union 1998), or have been separated in the genus Cissilopha (Hellmayr 1934, Blake and Vaurie 1962). Some common characteristics among these species are cooperative breeding, attendance on army ant swarms, and a Central American range (Howell and Webb 1995).
Bonaccorso et al. (2010) constructed a phylogeny of Cyanocorax (sensu lato) New World jays based on a phylogenetic analysis of DNA sequence data from five genes, both mitochondrial and nuclear: NADH Dehydrogenase Subunit 2 (ND2; 1002 base pairs); cytochrome b (cyt b; 999 base pairs); the Adenylate Kinase gene, intron 5 (AK5); the ß-Fibrinogen intron 7 (ßfib7); and TGFß2.5. The "Cissilopha" species formed a monophlyetic clade, sister to the core species of Cyanocorax. The basal member of this four-species clade is melanocyaneus.