Using a set of cranial morphometric characters, trends of variation in multivariate fluctuating asymmetry were evaluated and compared in populations of African fruit bats Rousettus egyptiacus and Eidolon helvum from the Gulf of Guinea islands, and the adjacent mainland. Levels of asymmetry were compared across populations and species, and significant differences were found in both comparisons. Differences coincided with species-specific patterns of morphological and genetic differentiation. Concordance of correlation matrices of asymmetry was also compared. Results were significant; concordance is hypothesized to be a by-product of developmental processes that produce the ‘fox-like’ morphology shared by these species. Consistency of asymmetry patterns suggests that the developmental pathway producing it is highly canalized. A prediction of the above hypothesis is that a radical change in the ‘fox-like’ structural pattern would result in breakage of the asymmetry parameter associated with it.