Three subspecies currently recognized:
cabanidis, described as Petasophora Cabanidis Heine 1863; type locality Costa Rica
Occurs in Costa Rica and Panama. Similar to nominate cyanotus, but sometimes has a blue wash on the breast (Dickey and van Rossem 1938).
cyanotus, described as Trochilus cyanotus Bourcier 1843; type locality Caracas
Occurs in the northern Andes.
crissalis, described as Colibri cyanotus crissalis Todd 1942; type locality Incachaca, Bolivia
Occurs in the central Andes. Zimmer (1950) characterized crissalis as an "unsatisfactory form", as "the separation [from cyanotus] is not pronounced or perfect", but on average crissalis differs from cyanotus in that the feathers of the undertail coverts are more extensively buff, with little or no green at the centers of these feathers (as is shown by cyanotus).
Phylogenetic analysis of DNA sequence data 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, 2008, 2014). Violetears (Colibri), including Lesser Violetear, belong to the mango clade. The sister to the violetears is Schistes geoffroyi (Wedge-billed Hummingbird). Within Colibri, the basal species appears to be serririrostris (White-vented Violetear); coruscans (Sparkling Violetear) is sister to the remaining species; and delphinae (Brown Violetear) is sister to the pair cyanotus + thalassinus (Mexican Violetear) (McGuire et al. 2014).
Early ornithologists (e.g. Ridgway 1911) considered thalassinus (monotypic) and cyanotus (polytypic) to be separate species, but Peters (1945) merged this into a single species, C. thalassinus, which became known as "Green Violetear". The differences in plumage between thalassinus and the taxa in the cyanotus group, however, are as great as those between cyanotus and the sympatric coruscans, and so these again are recognized as distinct species (Chesser et al. 2016; see also Remsen et al. 2015).