Seven subspecies are usually recognized (Storer 1970). In general, subspecies that are west of the Andes are smaller, have a reduced crest, and a darker head (Ridgely and Tudor 1989).:
E. p. pallida: Richer yellow on chest, head and throat are a darker gray (Isler and Isler 1999). Occurs southeastern Mexico to eastern Guatemala.
E. p. spodocephala: Underparts are a deeper, orangish yellow (Isler and Isler 1999). Nicaragua, and the Pacific Slope of Costa Rica.
E. p. stictothorax: Head is greenish olive instead of gray, throat is yellowish olive,and lacks a prominent crest (Isler and Isler 1999, Skutch 1954). Southwestern Costa Rica and western Panama.
E. p. cristata: Pale gray crest, olive-tinged throat (Restall et al. 2006). Eastern Panama, northern Colombia.
E. p. affinis: Long crest, but shorter than E. p. cristata and E. p. penicillata and with less white on the tips, paler throat (Isler and Isler 1999, Restall et al. 2006). Northern Venezuela.
E. p. penicillata: Has the largest crest, a white chin and throat (Restall et al. 2006). Southeast Colombia south to eastern Peru, and east to the Guyanas and northern Brazil.
E. p. albicollis: Head, throat, and the very long crest are a "buffy gray" (Isler and Isler 1999). Eastern Bolivia, northern Paraguay, northeast Argentina, and south central Brazil.
Burns and Racicot (2009) sequenced DNA from three individuals of the Gray-headed Tanager, two from adjacent populations in Bolivia and one from Panama. The two Bolivian individuals were very similar to each other, but the Panamanian sample differed in 4.8% of the base pairs sequenced, a level higher than that observed between many avian species and genera. Thus, multiple independent evolutionary units that perhaps represent distinct species may exist within the Gray-headed Tanager.