The genus Molossus of the free-tailed bat family Molossidae is morphologically conservative and the level of genetic divergence is also low among many species, which has masked the actual species diversity in the genus. We analyzed the evolutionary relationships among species within Molossus using three mitochondrial (COI, Cytb, and 16S RNA), and two nuclear genes (RAG2 and β-fib) from more than 400 specimens across the Neotropics. We also investigated the genetic integrity of currently recognized species, especially those with broad geographic distributions and controversial taxonomic arrangements. Maximum likelihood and Bayesian phylogenetic reconstructions show that some recognized species are not monophyletic. The use of combined mitochondrial and nuclear genes as well as the use of only mitochondrial markers revealed more robust phylogenies than those for individual data sets and those restricted to the two nuclear genes. We recovered the recently described M. fentoni and M. alvarezi, validated M. milleri and M. verrilli as distinct species relative to M. molossus, and confirmed that the name M. barnesi should be considered as a junior synonym of M. coibensis. Additionally, M. rufus appears to be a complex of cryptic species, showing that the broadly distributed genus Molossus is more diverse than previously reported.