Interand intraspecific variation of fruit bats of the genus Rousettusin Iran were examined. Morphometric analyses of 7 external and 21 craniodental characters of material from southeast Iran showed that two species are found there, R. aegyptiacusand R. leschenaultii.Phylogenetic trees inferred from Bayesian inference and maximum likelihood analyses of the mitochondrial cytochrome b (cyt b) marker revealed that R. aegyptiacuspopulations are divided into five lineages and the Iranian population clustered with the Middle East samples. The result showed very low genetic variation between different populations of R. leschenaultiithroughout its range in the Palaearctic and Indo-Malayan realms.