The lesser yellow-shouldered bat, Sturnira nana, is a member of the most diverse genus of the New World leaf-nosed bats (Phyllostomidae). This species was considered endemic to Peru until 2009 when researchers captured a series of individuals in the Cordillera del Cóndor of southeastern Ecuador and identified them as S. nana. To assess the taxonomic status of this Ecuadorian population in relation to S. nana from Peru, we analyzed cytochrome b gene sequences and craniodental measurement data. In addition, we used principal component analysis to elucidate differences in climatic niches. Our analyses suggest that populations currently identified as S. nana from Ecuador and Peru are genetically, morphologically, and ecologically divergent. Herein, we formally describe the population of small Sturnira from Ecuador as a new species.