We present information on the morphological structure and measurements of the os penis for eight families and 28 species of bats occurring on Madagascar, most being endemic to the island. For one of these families, Miniopteridae, no bacular structure was found and for a second family, Emballonuridae, the structure was absent in one species (Taphozous mauritianus). For the majority of taxa, the descriptions and measurements given herein of their respective bacula are presented for the first time in the published literature. In cases when samples are sufficient for certain species, we examine intra-specific variation in bacular morphology. For species the subject of previous published phylogeographical studies and which showed clade structure associated with elevational or latitudinal clines, we investigate if intra-specific differences in bacular structure are correlated with clade associations. We examine possible correlates associated with os penis measurements and, in general, across all species or within certain families, there was not a clear correlation between body size, as measured by forearm length, and different bacular measurements.