Eugenes fulgens is monotypic.
Described as Trochilus fulgens Swainson 1827; type locality Temascáltepec, Mexico
Eugenes viridiceps Boucard 1878 usually is regarded as a junior synonym of nominate fulgens, but is recognized by some authors (e.g. Peters 1945) as a valid subspecies, occupying the southern portion of the range of the species (southern Mexico, south of the Isthmus to Tehuantepec, south to northern Nicaragua).
Eugenes spectabilis (Talamanca Hummingbird) of Costa Rica and Panama long was classified as a subspecies of Eugenes fulgens, under the English name Magnificent Hummingbird. These two taxa now are recognized as a separate species "on the basis of differences in plumage commensurate with those between other sister species of hummingbirds" (Chesser et al. 2017).
Phylogenetic analysis of DNA sequence data, from both mitochondrial and nuclear genes, groups all hummingbirds into nine clades (McGuire et al. 2007, 2008, 2014). Eugenes is a member of what these authors called the mountain-gem clade Lampornithini), together with Lamprolaima, Heliomaster, Panterpe, and Lampornis. Within this group, Eugenes is sister to Lamprolaima rhami (Garnet-throated Hummingbird); the Lamprolaima + Eugenes clade is sister to the clade of Heliomaster + Panterpe; and Lampornis is sister to the Lamprolaima + Eugenes + Heliomaster + Panterpe group (McGuire et al. 2014).