At least three subspecies have been described (Wetmore et al. 1984). Storer (1970) recognized two subspecies, but Wetmore et al. (1984) considered the species to be monotypic.
florida (Sclater and Salvin 1869). Type locality Costa Rica. See Detailed Description. Caribbean slope of Costa Rica and western Panama.
auriceps Chapman 1914. Type locality Buenavista, Nariño, Colombia. Extreme eastern Panama south to northwestern Ecuador. Similar to florida, but with more extensive yellow on the crown, reaching to the middle of the eyes. In addition, the greenish edges of the scapulars are narrower, or non-existent (Hellmayr 1936).
The Emerald 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 classified the Emerald Tanager within group 5, the largest species group, along with seven other species: Blue-whiskered Tanager (T. johannae), Green-and-gold Tanager (T. schrankii), Golden Tanager (T. arthus), Silver-throated Tanager (T. icterocephala), Saffron-crowned Tanager (T. xanthocephala), Golden-eared Tanager (T. chrysotis), and Flame-faced Tanager (T. parzudakii). All of these species except T. parzudakii have a striped back, all are forest dwelling, and six of the eight species (including the Emerald Tanager) have a consistent, diagonal-lean foraging method (Isler and Isler 1987). Monophyly of the this species group has been upheld using molecular data, specifically cytochrome b and NADH dehydrogenase subunit 2 genes of the mitochondria (Burns and Naoki 2004, Sedano and Burns 2010). The Emerald Tanager is most closely related to the Silver-throated Tanager (Tangara icterocephala) (Burns and Naoki 2004, Sedano and Burns 2010).