Two subspecies of the Resplendent Quetzal are recognized (Clements 2007). The southern subspecies costaricensis inhabits Costa Rica and the western highlands of Panama, while nominate mocinno occurs in southern Mexico, Honduras, eastern El Salvador, and northcentral Nicaraugua. The subspecies costaricensis generally is smaller (see Measurements); the uppertail coverts of the male are shorter and narrower; and it is less golden in tone (Johnsgard 2000).
Johnsgard (2000) describes the Resplendent Quetzal as a "very near relative of the Crested Quetzal [Pharomachrus antisianus]." Some sources consider the Crested Quetzal to be a race of the Resplendent Quetzal (e.g. Peters 1945), or that the two form a superspecies.
Pharomachrus quetzals form a clade together with the Eared Quetzal Euptilotis neoxenus (Espinosa de los Monteros 1998, Moyle 2005), which in turn is part of a New World clade of trogons. Espinosa de los Monteros (1998) hypothesized that the New World clade is a sister group to the Asian trogons, and that the African trogons were basal to all other trogons. Moyle (2005), however, found evidence that the New World trogons are the basal clade in Trogonidae, and that the African and Asian clades are sister to one another. The quetzal clade is believed to have radiated from where it arose in the Andes, with the Resplendent Quetzal as the youngest of the species (Collar 2001).