Tangara cyanoptera is part of the Order Passeriformes and the Family Thraupidae (Clements 2013). Tangara cyanoptera is a member of the speciose genus Tangara. This genus includes more species than any other genus of exclusively neotropical birds (Isler and Isler 1987). Isler and Isler (1987) subdivided Tangara into 13 species groupings based on geographic range, appearance, behaviors (with an emphasis on foraging behaviors), vocalizations, and nest sites. The Black-headed Tanager belongs to Isler and Isler’s species group 12 along with T. viridicollis, T. argyrofenges, and T. heieni. Isler and Isler (1987) also included Tangara pulcherrima in this species group due to similarities in plumage between T. pulcherrima and T. cyanoptera. However, genetic data show that T. pulcherrima is only distantly related to other Tangara tanagers; thus, T. pulcherrima is currently considered the sole member of the genus Iridophanes, closely related to other ‘black and yellow’ tanagers (Burns et al. 2003, Burns et al. 2014). In addition, when Graves and Weske (1987) described Tangara phillipsi (not included in Isler and Isler (1987)), they argued that it was part of a “black-capped” group that contained T. argyrofenges, T. heinei, and T. viridicollis. DNA sequence data confirms monophyly of a modified group 12 (excluding T. pulcherrima, but including T. phillipsi). Within this group, T. cyanoptera is sister to a clade containing T. argyrofenges, T. heinei, T. phillipsi, and T. viridicollis (Burns and Naoki 2004, Sedano and Burns 2010, Burns et al. 2014). Given its phylogenetic position, Sedano and Burns (2010) concluded that this species is one of three ‘core’ tanagers in which dispersal into the Tepuis can be inferred.
The genus Tangara is paraphyletic with respect to Thraupis (Sedano and Burns 2010, Burns et al. 2014). As a result, Sedano and Burns (2010) suggest moving many species of Thraupis into Tangara, including Thraupis cyanoptera. Given that this species has the same specific eptithet as Tangara cyanoptera, a new name is needed for Tangara cyanoptera because its name post-dates Thraupis cyanoptera. Thus, Sedano and Burns (2010) suggest the junior synonym Tangara argentea be used for this species in the future. A more complete DNA analysis of the tanagers supported this recommendation (Burns et al. 2014).
The Black-headed Tanager is split into two subspecies, Tangara cyanoptera cyanoptera and Tangara cyanoptera whitelyi. These two species may possible constitute two separate species based on their plumage and habitat differences and geographic isolation from each other (Hilty 2011), but genetic data are needed to further investigate this question.