Phylogenetic relations among five species of Hipposideridae and seven species of Rhinolophidae including one endemic species (Rhinolophus rex) were examined by partially sequencing of the mitochondrial cytochrome b gene (528 bp). Analyses of the cytochrome b sequences of Hipposideridae and Rhinolophidae suggest that each formed a monophyletic group. All phylogenetic analyses indicate that Aselliscus should remain as a genus within Hipposideridae, with the mean percentage sequence differences (16.43%) and transition: transversion ratios (2.032) between Aselliscus and Hipposideros. Within Hipposideros, H. armiger shows close affinity to H. larvatus although it possesses superficial similarity morphological characters to H. pratti. Genetic distance values suggest that H. larvatus and H. armiger diverged from each other approximately 1.7-4.3 million years ago, and H. pratti diverged from the larvatus-armiger clade approximately 2.1-5.2 million years ago.