Three subspecies of Red-necked Tanager currently are arecognized (Storer 1970, Isler and Isler 1987, Clements et al. 2010):
cearensis Cory 1916; type locality Serra Baturité, Ceará, Brazil
This subspecies occurs in Ceará, northeastern Brazil and differs from the other two by a more purplish crown, black plumage on the upper throat between the red collar and blue lower throat, and some sky-blue feathers on the upper tail coverts (Hellmayr 1936, Nørgaard-Olesen 1973).
corallina (Berlepsch 1903); type locality Bahia, Brazil
This subspecies occurs in the coastal region of northeastern Brazil in Pernambuco and Alagoas and possibly southward to northwest Bahia. Similar to nominate cyanocephala, but smaller; the red collar is paler and yellow band on the wing is narrower. Underparts are more yellowish (Hellmayr 1936, Nørgaard-Olesen 1973).
cyanocephala (Müller 1776); type locality Cayenne; error, Rio de Janeiro substituted by Berlepsch 1912
This subspecies occurs in the coastal region of southeastern Brazil to eastern Paraguay and northeaster Argentina (Missiones). See Detailed Description.
The Red-necked Tanager is classified in the genus Tangara, the largest genus of Neotropical birds. Tangara is divided into 13 species groups based on vocalizations, diet, geographic distributions, behavior, and appearance (Isler and Isler 1987). Isler and Isler (1987) placed the Red-necked Tanager in Species Group 4, along with the Brassy-breasted Tanager (T. demaresti) and the Gilt-edged Tanager (T. cyanoventris). These species all occur in eastern Brazil. Isler and Isler (1987) suggested that these three species may be closely related to members of Species Group 3 (Paradise Tanager T. chilensis), Seven-colored Tanager T. fastuosa, and Green-headed Tanager T. seledon). In general, phylogenetic analyses of DNA sequence data agree with these suggestions (Naoki and Burns 2004, Sedano and Burns 2010). With the exception of T. chilensis, all of these species form a strongly supported monophyletic group. Within this group, the exact position of T. cyanocephala is unclear. It is either most closely related to a clade containing T. cyanoventris and T. desmaresti, or to a clade containing T. fastuosa and T. seledon (Sedano and Burns 2010).