We tested the effects of aspect ratio, wing loading and body size (forearm length) on four estimators of molecular diversity (based on mitochondrial D-loop and cytochrome-b DNA sequences) among eight Afro-Malagasy species of free-tailed (Family Molossidae) bats. As expected based on many previous animal studies conducted at broader taxonomic scales, F_ST was significantly negatively correlated with wing loading (a good proxy for dispersal ability), even after correcting for phylogeny. However, haplotype diversity, nucleotide diversity and k (the mean number of nucleotide differences between sequences) were not significantly correlated with body size, aspect ratio or wing loading. According to the metabolic rate hypothesis, we expected a significant negative correlation between k and body size. No such significant correlation was obtained, which is attributed to species differences in population size and the timing of past bottlenecks inferred from population demographic data.