The original description for Anoura fistulata (long-lipped bat) was mostly qualitative in nature. Here we make a quantitative reassessment of morphological variation in skull shape for this and other Ecuadorian species. Our goal is to provide a perspective into morphospace for understanding the boundaries and extent of variation within and among species of Anoura occurring in Ecuador. Our results show that, besides its singular differences in soft-tissue anatomy, the distribution of samples in morphospace for A. fistulata suggests this species occupies an intermediate space between A. geoffroyi and A. caudifer. Anoura geoffroyi and A. caudifer share opposite regions of morphospace, where size is the largest factor contributing to variation, and along the shape vector both species are distinguished mostly by a contraction of the maxilla and a contraction of the braincase, respectively. Although size is the main factor determining boundaries among species, for A. cultrata shape seems to be more relevant, as its geometric configuration of the skull is remarkably different. The other species are similar in shape when size is factored out. An unusual group of specimens may require further study as they may represent an unknown species, as these occupy unexpected areas of morphospace. A discussion of why we do not think there is evidence to assign this unusual group to any of the small species of Anoura (i.e. A. caudifer, A. aequatoris, and A. luismanueli) is also included. Populations of A. geoffroyi from the western and eastern slopes of the Andes show statistically supported differences in most of the measured morphological traits, however this is not true for A. caudifer. The effect of western and eastern habitats on the geometric configuration of the skull is different and inverted between both species. This results in a statistical interaction between the two slopes of the Andes and the two species. Eastern populations of A. geoffroyi and A. caudifer are morphologically closer than western populations in both species. Anoura geoffroyi possesses a larger altitudinal range and a larger body size, a positive correlation that may concur with the hypothesis of body size serving as a buffer to extreme or highly variable environments. The frequency distribution of character states in morphospace and their differentiation across the various species of Anoura is discussed in the context of diet and habitat.