We examine patterns of morphological and genetic variation in Chaerephon leucogaster (family Molossidae) on Madagascar, Mayotte in the Comoros Archipelago, and the offshore Tanzanian island of Pemba. Five external, 10 cranial, and eight dental measurements of animals from different Malagasy populations (grouped according to bioclimatic regions) show differences in the degree of sexual dimorphism and size variation. Further, the population on Mayotte is largely identical in size to those from western Madagascar, and animals from Pemba are notably larger than those from Madagascar and Mayotte. Cytochrome b genetic distances across samples from these islands were low (maximum 0.0035) and animals from Pemba and Mayotte shared cytochrome b haplotypes with Malagasy bats. D-loop data showed some concordance between haplotype distribution, geographical position (latitude and island), and the bioclimatic zones. Animals from Pemba and Mayotte formed a unique D-loop haplotype, which was a minimum of six mutational steps different from Malagasy haplotypes. Within Madagascar, certain haplotypes were exclusive to the north (13°S latitude band) and arid southwest (22° and 23°S latitudes) regions. In general, there was no clear concordance between variation in haplotype distribution, latitude, altitude or gender. Where concordance occurred, the genetic distances involved were not sufficiently high to warrant the definition of new taxonomic units. Hence, based on current genetic information, patterns of morphological variation of the Madagascar populations and differences between Pemba and Mayotte/Madagascar are best explained as inter-population variation and may be adaptive, associated with different climatic regimes and associated ecological variables.