Nine subspecies of the Bay-headed Tanager are recognized (Storer 1970, Clements et al. 2009). These nine subspecies sometimes are sorted into three subspecies groups (e.g., Sibley and Monroe 1990, American Ornithologists' Union 1998), as follows:
albertinae group (called the gyroloides group by Sibley and Monroe 1990 and the American Ornithologists' Union 19998) - Includes six subspecies. All have a blue rump and blue underparts.
T. g. bangsi - The yellow of the nuchal collar and of the wing coverts is reduced (Hellmayr 1936). Occurs in Costa Rica and in western Panama, east to Coclé; populations in the Canal Zone and in eastern part of the province of Panamá show characters that are intermediate between bangsi and deliticia (Storer 1970, Wetmore et al. 1984).
T. g. deleticia - The yellow nuchal band and yellow on the wing coverts are absent or almost absent. Occurs in eastern Panama (Darién) and in the western and central Andes of Colombia, east to the west slope of the eastern Andes of Colombia (Storer 1970, Hilty and Brown 1986).
T. g. nupera –Similar to bangsi, from which "differs merely by somewhat paler ... head and slightly lighter, more greenish blue of the under parts" (Hellmayr 1936). Occurs from the western slope of the western Andes of southern Colombia in Nariño, south through western Ecuador to extreme northwestern Peru in Tumbes (Storer 1970, Wiedenfeld et al. 1985, Hilty and Brown 1986, Ridgely and Greenfield 2001).
T.g. catharinae – This subspecies a green throat, but an extensive blue area in the lower breast and belly. It is somewhat similar to nominate gyrola, but "yellow nuchal collar much wider, the head much darker ... [has] a light cerulean blue patch on the rump, and the under parts much more extensively blue" (Hellmayr 1936). Occurs on the east slope of the Andes from southern Colombia (Meta south) south through the Andes of Ecuador and Peru to central Bolivia in Cochabamba and Santa Cruz (Storer 1970).
T. g. parva – This subspecies a green throat, but an extensive blue area in the lower breast and belly. It is much like catharinae, "but wing and tail shorter; adult males with brown of cap averaging darker; yellow of collar and shoulder slightly lighter; blue of rump and under parts and green of back averaging a little lighter" (Zimmer 1943). Occurs from the lowlands of southeastern Colombia and southern Venezuela south to Peru (south at least to Pasco) and east to western Brazil north of the Amazon (Zimmer 1943, Storer 1970).
T. g. albertinae- Similar to catharinae, but the most distinctive feature is that the wing coverts are rufous rather than yellow or yellowish green. Also the nuchal band is indistinct, and the "hind neck and upper back [are] much more yellowish" (Hellmayr 1936). Occurs in western Brazil south of the Amazon (Storer 1970).
viridissima group - Two subspecies. These two subspecies are almost entirely green, except for the chestnut head; the rump and underparts both are entirely green; and the yellow of the nuchal band and of the wing coverts is reduced or absent.
T. g. toddi – Occurs in northern Colombia in the Santa Marta mountains, on the east slope of the eastern Andes in Norte de Santander and northern Boyacá, in the Andes of Venezuela, and in the coastal cordilleras of Venezuela east to Miranda (Storer 1970, Hilty and Brown 1986, Hilty 2003).
T. g. viridissima – Very similar to toddi, but the rufous of the head is darker, and the underparts are more bluish green (Hellmayr 1936). Occurs on Trinidad; populations in the eastern coastal cordilleras of Venezuela in Anzoátegui, Monagas, and Sucre are intermediate between viridissima and toddi (Storer 1970).
gyrola group - One subspecies, which has a green rump, a green throat, and an extensive blue area on the lower breast and belly.
T. g. gyrola – See Detailed Description. It occurs in southern Venezuela and adjacent northern Brazil east across the Guianas to Amapá, Brazil (Storer et al. 1970, Novaes 1978).
In addition to the above descriptions, the following table (from Nørgaard-Olesen 1973) can be used to separate the subspecies: