Sánchez-Osés (2003) evaluated 49 individuals and concluded that Black Inca is monotypic, with no geographic variation in color pattern. Nevertheless Sánchez-Osés (2003) observed small but not statistically significant differences in the length of the tail and in the depth of the fork; approximately 47% of the specimens had reliable geographic information on the labels and so he recognized two geographical pools: Virolín in the department of Santander and Pedro Palo in the department of Cundinamarca.
Described as Trochilus prunellei (Bourcier 1843); type locality Facatativá [Cundinamarca]. Colombia.
Sánchez-Osés (2003) considered Coeligena prunellei as monotypic and summarized the different generic names by which this species has been known: Bonaparte (1850) included this species in the genus Bourcieria, and it later was assigned by Reichenbach (1853) to the subgenus Homophania. Gould (1861) assigned this species to the genus Lamproygia. Hartert (1910) and Berlioz (1936) classified prunellei as a species of Helianthea. Peters (1945) classified this species as Coeligena prunellei, which continues to be the accepted name for this taxon (e.g. Meyer de Schauensee 1966, Fjeldså and Krabbe 1990 Schuchmann 1999).
A phylogenetic analysis of Coeligena, based on phenotypic characters, placed prunellei as a member of the coeligena-wilsoni clade (Sánchez-Osés 2003). Parra et al. (2009) confirmed, using genetic data, that these three taxa are sister species.