This study investigated allozyme and morphometric variability within the genus Cynopterus, with particular emphasis on C. nusatenggara, which is endemic to Wallacea, the area encompassing the Oriental-Australian biogeographic interface. The genetic distances between Cynopterus species are small by mammalian standards and suggest that this genus has undergone a recent series of speciation events. The genetic distance between populations of C. nusatenggara is strongly correlated with both the contemporary sea-crossing distance between islands and the estimated sea crossing at the time of the last Pleistocene glacial maximum, 18,000 B.P. This observation, together with low levels of population substructure within islands as shown by F-statistics, indicates that the sea is a primary and formidable barrier to gene exchange. The genetic distance and the great-circle populations of C. nusatenggara are not correlated, although a principal-coordinates analysis of genetic distance reveals relationships between the populations that are similar to their geographical arrangement. A strong negative correlation exists between the level of heterozygosity within island populations of C. nusatenggara and the minimum sea-crossing distance to the nearest large source population. This is interpreted as reflecting an isolation effect of the sea, leading to reduced heterozygosity in populations that have larger sea barriers between them and the large source islands. Independently of this, heterozygosity is negatively associated with longitude, which in turn is associated with systematic changes in the environment such as a gradual decline in rainfall from west to east. The association between heterozygosity and longitude is interpreted as reflecting an association between genetic and environmental variance and supports the niche-width theory of genetic variance. Morphometric variability did not show any of the main effects demonstrated in the genetic data. Furthermore, there was no evidence that, at the level of individuals, genetic and morphometric variability were associated.