Molossid bats exhibit a great diversity of size and skull morphology which likely reflect a trophic function and may be indicative of the degree of resource partitioning and overlap. We explored the morphofunctional variation of the skull in molossid species from Argentina, where 18 species had been recorded, and are representative of the vast South American Southern Cone region. We measured 18 craniodental variables in 377 specimens representing all 18 species. We performed a multivariate analysis using craniodental variables, and we used a comparative phylogenetic method, to determine the importance of phylogeny in morphofunctional variation. The specimens distribution in morphospace showed a clear segregation between species on the basis of skull size and morphological differences related with prey selection, and associated with other important factors such as echolocation and flight. We show that the morphological pattern observed was determined principally by the evolutionary history of the family, we identified major events of expansion of occupied morphospace with the origination of large species such as those in Eumops as well as small species of Molossops and Cynomops. We believe that the joint effects of history, size and functional morphology busted the evolution of Neotropical molossids and facilitated the coexistence of related species.