Storer (1970) recognized six subspecies; the following descriptions taken are from Restall et al. (2006) except where noted:
T. g. bogotensis (Andes of eastern Colombia and northwestern Venezuela): as described above.
T. g. chrysophrys (coastal mountains of Venezuela; interior highlands of southern Venezuela in Amazonas and southwestern Bolívar, and immediately adjacent Brazil): adult bright yellow-green above, with yellow forehead and eyebrow/eyering more pronounced; juvenile dull yellowish green above, washed dingy yellowish below, with streaks instead of spots.
T. g. eusticta (Costa Rica and Panama): Similar to T. g. guttata, however underparts bear more spots, particularly the throat. Feather edgings on throat and breast are pale glaucous green; green color on flanks is more extended and brighter; edgings of remiges and wing coverts appear beryl-green (Todd 1909).
T.g. guttata (interior highlands of southern Venezuela in southeastern Bolívar, and immediately adjacent Brazil): above like bogotensis, below like chrysophrys, but throat unmarked, black spots below smaller.
T.g. tomilae (central Andes of Colombia): like bogotensis, but throat and breast much more heavily spotted; undertail coverts have broad black shaft streaks.
T. g. trinitatis (Trinidad): like chrysophrys but deeper golden-yellow on forehead and eyebrow, larger spots both above and below, including on throat.
The Speckled Tanager is a member of Tangara, which contains 49 species, and is the largest genus of Neotropical birds (Isler and Isler 1999). Within Tangara, T. guttata is sister to the Yellow-bellied Tanager (T. xanthogastra), and these two form a clade with three very similar species: Spotted Tanager (T. punctata), Rufous-throated Tanager (T. rufigula), and Dotted Tanager (T. varia) (Burns and Naoki 2004). Isler and Isler (1999) grouped these birds together under their Tangara "Species Group 6," citing many features in common including their plumage, and a primary preference for foraging in the high canopy. This clade in turn is sister to a larger clade containing 22 species, including the genus Thraupis and other members of Tangara (Sedano and Burns 2010). Recent phylogenetic work found that the monophyletic group containing Tangara and Thraupis are sister to a clade containing many Andean highland tanagers including members of the genera Anisognathus, Buthraupis, and Bangsia (Sedano and Burns 2010). Within Thraupidae, the clade containing Tangara, the type genus Thraupis, and the highland clade described above, are considered ‘core tanagers,’ because they contain species that are typical of the group (Burns and Naoki 2004, Sedano and Burns 2010).
The Speckled Tanager has also been known as the Yellow-browed Tanager (Skutch 1954), and the Speckled Calliste (Slud 1964). The same species has also been known under several different scientific names, including T. chrysophrys (Stiles and Skutch 1991).