The taxonomic status of the greater mouse-tailed bat (Rhinopoma microphyllum) in Iran is not clear and researchers have reported conflicting results. The initial suggestion of the presence of two subspecies R. m. microphyllum and R. m. harrisoni has been questioned on the basis of small differences between the populations. These differing inferences are based on analysis of morphological characteristics. Here we present a study of the phylogeography of this species using 567 bp of the mitochondrial control region in several localities in Iran and from across its distribution to infer the taxonomic status of this species. Based on the control region sequences, we found high genetic diversity in the Iranian population but variation between populations was not statistically significant. The phylogenetic trees and statistical parsimony network showed all Iranian samples were grouped in the same clade and Levant samples belonged to another clade. These results support the hypothesis that all Iranian specimens belong to one subspecies. We therefore recommend that R. m. microphyllum and R. m. harrisoni can be synonymized as the same subspecies with the name R. m. harrisoni, because molecular results indicate that Iranian samples differ from Levant and Moroccan samples (R. m. microphyllum).