Throughout the Old World Tropics, examples of cryptic diversity have been demonstrated in leaf-nosed bats from the Family Hipposideridae. In addition to cryptic diversity, the widespread distributions and graded morphologies of some species render the taxonomy of this family poorly resolved. We used sequences of the mitochondrial gene ND2 and the nuclear gene RAG1 to reconstruct molecular phylogenetic relationships for hipposiderid species. Specimens from Solomon Island and Cape York Peninsula, Australia, were sequenced and combined with published sequences from Southeast Asia. Our results suggest the presence of undescribed diversity in northern Australia. Sequences of ND2 and RAG1 for samples of Cape York Hipposideros ater were distinct from those of Southeast Asia, with corrected sequence divergence estimates for the mitochondrial gene exceeding 23%. In comparison, there was no cryptic diversity detected in Solomon Island specimens when compared to conspecifics from Southeast Asia. On the contrary, three species members of the diadema morphological group from the region exhibit variability in the mitochondrial gene ND2, far below that of other species included in the analyses.