There is slight geographic variation in Eriocnemis mosquera, and a name, bogotensis Hartert 1897, has been applied to the northern populations, on the basis of a slightly longer bill and greener (less coppery) plumage. Bill length in males appears to be clinal, however, and so the species currently is treated as monotypic (Bleiweiss 1988).
Described as Trochilus Mosquera (DeLattre and Bourcier 1846); type locality Pasto, Colombia.
A recent phylogenetic survey of the phylogenetic relationships of hummingbirds, based on DNA sequence data from both mitochondrial and nuclear genes, reveals that hummingbirds (Trochilidae) constitute nine major clades, comprising the hermits, mangos, Patagona, topazes, coquettes, brilliants, mountain-gems, bees, and emeralds (McGuire et al. 2007, 2009). Eriocnemis belongs to the brilliant clade, and is sister to Haplophaedia; the relationship of Eriocnemis + Haplophaedia to other genera in this clade is not well resolved. Other genera in the brilliant clade are Aglaeactis, Coeligena, Lafresnaya, Ensifera, Pterophanes, Boissonneaua, Ocreatus, Urosticte, Urochroa, and Heliodoxa (McGuire et al. 2007, 2009). This study including representatives of only 4 of the 11 species of Eriocnemis; within this small sample, Eriocnemis mosquera is identified as sister to Eriocnemis vestita (Glowing Puffleg) (McGuire et al. 2007, 2009).