Rhinopoma muscatellum is one of the six species of mouse-tailed bats (Rhinopomatidae) that is common in Iran with over 70 reported localities. We investigated phylogeographic relationships and evolutionary history in this species from Iran using two mitochondrial DNA markers, D-loop region (D-loop, 464 bp) and cytochrome b (Cytb, 726 bp). We found a low degree of genetic diversity in the Iranian populations of R. muscatellum (π = 0.0061 for D-loop and π = 0.0013 for Cytb), that shows the presence of inbreeding and close relationship among the haplotypes. The average genetic divergence between Iranian populations was 0.01–0.57% in D-loop and 0.00–0.14% in Cytb. Here, the phylogenetic trees and statistical parsimony network showed all Iranian samples were grouped in the same clade as R. muscatellum seianum. Results of mismatch distribution analysis, neutrality test, and haplotype networks indicated a recent population expansion. The Bayesian skyline plots based on D-loop and Cytb also showed patterns of population expansion, initiating around 9–6 kyr and 15 kyr, respectively. Time to the most recent common ancestor of the Iranian haplotype was estimated to be between 0.82 to 0.17 Ma (Cytb data).