A total of 111 adult specimens of Bearded Tomb Bats (Taphozous spp.) was examined morphologically and 58 were examined by protein electrophoresis from recent collections made from islands in Nusa Tenggara (Lombok, Sumbawa, Moyo, Alor, Timor, Semau, Roti and Savu).Multiple regression analysis revealed no significant sexual dimorphism; of the 30 characters considered, four skull characters were influenced by the age of adults as determined by their molar tooth wear. Principal component analysis produced two distinct clusters of specimens. These clusters relate to the species Taphozous melanopogon Temminck, 1841 and T. achates Thomas, 1915. Canonical variate (discriminant) analysis of skull characters alone allowed allocation of 100 percent of cases to their correct species. The Rotinese population of T. achates differs somewhat morphologically from those of Savu and Semau.Protein electrophoresis revealed that nine of the 31 loci scored were variable within or between populations. The measured average heterozygosity within populations ranged from 0.039 on Lombok I. to zero on Semau and Savu I. Two of the nine variable loci showed highly significant interpopulation variation (Gox and Pep-B).The genetic data separate the same two broad groups as indicated by the morphological analysis (T. melanopogon and T. achates). Although the average genetic distance between these two species is small (Nei distance 0.031) there is a low level of intrapopulation variation.Taphozous melanopogon and T. achates are rediagnosed. The morphological and genetic variation of these taxa are discussed in the context of the historical biogeography of their island populations.