Tenuous descriptions of many species and subspecies of mastiff bats make the taxonomy of MolossusE. Geoffroy, 1805 confusing and unstable. Molossus is one of the most diverse genera of free tailed bats in the pantropical family Molossidae Gervais, 1856. Given their impressive variation due to geography, sex, and ontogeny, and incomplete knowledge about species boundaries, a comprehensive taxonomic revision of the genus is needed. In addition, the level of genetic divergence, even among morphologically well-characterized species is low, often making diagnosis of groups difficult and likely resulting in an underestimation of the number of species. Brazil has a wide territory harboring many different physiognomies, but with no study focusing on the morphological variation and taxonomy of Molossus available. Therefore, we have analyzed qualitative and quantitative characters from 493 specimens belonging to nine species of Molossus, and conducted a wide comparative morphological analysis of the species occurring in Brazil. In addition, we propose a hypothesis of phylogenetic relationships within Molossus based on morphology, establishing the morphological characters for diagnosis and identification of species, and update the geographic distribution of Molossus species in Brazil, with range extensions for four taxa. Six species, Molossus rufusE. Geoffroy, 1805, Molossus molossus (Pallas, 1776), Molossus coibensisAllen, 1904, Molossus aztecusSaussure, 1860, Molossus currentiumThomas, 1901, and Molossus pretiosusMiller, 1902 occur in Brazil. We bring support for the synonymy of Molossus bondaeAllen, 1904 with M. currentium, as suggested by several authors.