Abstract Genetic and morphometric variation was examined in eleven island populations of the horse-shoe bat, Rhinolophus affinis, at the easterly end of this widespread species’ range and encompassing the Australian–Oriental biogeographic interface. Allozyme variation revealed mean heterozygosity levels within islands of 0.047, which is near the mammalian average. However, heterozygosity tended to decline from west to east as populations approached the periphery of the species’ distribution, and was lowest in those islands that were separated by the greatest sea-crossing from source populations. There is extensive between-island genetic differentiation (mean FST = 0.40) and relationships between islands are associated with their arrangement in geographical space; genetic distance is correlated with geographical distance and the genetic arrangement of islands is associated with longitude. The arrangement of islands as indicated by variation in body and skull metrics is also associated with their geographical positions, and the metric and genetic measures are themselves associated. While other taxa in the region have shown genetic-geographical concordances, R. affinis is the only one that displays concordant patterns in metrical features. These patterns in biological diversity are interpreted as arising from the sequential island population structure and clines in key biogeographic gradients.