Extant Malagasy members of the genus Macronycteris are broadly distributed across the island and vary in size with respect to sex, bioclimatic zone, and intraspecific clade affinity. An extinct Quaternary species, M. besaoka, was considered morphologically distinct from modern Macronycteris based on its robust mandibles and wider molars. Since its description, taxonomic and phylogenetic revisions have reshaped our understanding of Malagasy Macronycteris. This included the discovery of the cryptic species M. cryptovalorona and the recognition of two clades within M. commersoni. Recent augmentation of museum cranial collections of Malagasy members of the genus has permitted renewed investigation into morphological trends. Herein, we examine craniodental morphology of modern Malagasy Macronycteris spp., and investigate the validity of M. besaoka through nonparametric multivariate methods. The results of this study support M. besaoka as a valid species. Further, some specimens previously diagnosed as M. besaoka are best associated with modern M. commersoni from the dry bioclimatic zone. These results have implications for the history of the bat community at Anjohibe Cave, as well as the identification of other Macronycteris subfossils from dry western Madagascar.