The short-tailed bats Carollia brevicaudum and C. perspicillata are two of the most abundant and widely distributed species of phyllostomids in the Neotropics. Many authors have found intraspecific variation throughout its distribution, mainly in body size and coloration. Since there is no consensus on the magnitude of intraspecific variation, in this study we assessed the variation patterns of seven populations of both C. brevicaudum (n = 185) and C. perspicillata (n = 190) from Peru and Ecuador. The populations were delimited by potential barriers of distribution such as the main eastern basins, the Amazonas River, and the Andes. We took 26 craniomandibular measurements and used univariate, multivariate, and cluster analyses. We found significant morphometric differences between certain pairs of populations of both species, but none are supported by all the analyses. The broad overlap of the variables in the populations evaluated of both species suggests a morphological complexity not related to the assessed geographies.