Previous studies conducted on morphological variation of the endemic Malagasy bat Hipposideros commersoni sensu stricto (Hipposideridae) revealed a north-south morphological cline, with larger individuals present in the north. Little is known about potential sexual differences in the echolocation calls of this species. We captured 59 adult individuals (24 males and 35 females) at different sites spanning the western half of Madagascar, measured their forearm length and recorded echolocation calls. These data were used to examine possible variation in echolocation calls and body size, which showed statistically significant differences. Male H. commersoni have an average forearm length of 93.1 mm and emit calls at 68.6 kHz, while the average measurements for females are 83.9 mm and about 72.9 kHz, respectively. Principal component analysis revealed variation in morphological and bioacoustic parameters, suggesting a high intraspecific variation. Regression analysis of intersexual data showed that females from the far north (Ankarana) significantly deviate from the allometric relationship by emitting echolocation calls lower than predicted by their size. These divergences may be associated with phenotypic variation, migratory movements or presence of a possible cryptic species. Detailed phylogenetic and phylogeographical analyses of the H. commersoni complex are needed to address these questions.