Molecular tools have confirmed the presence of morphologically cryptic bat species initially detected by divergent echolocation calls. Here we document the presence of two sympatric, genetically distinct populations of bats whose echolocation calls were similar in peak frequency. They differed only slightly with respect to size, skull and wing morphology, and noseleaf shape, but the individuals, all initially identified as Rhinolophus arcuatus, fell into two groups exhibiting 3–4% sequence divergence in the cytochrome b gene. The coexistence of cryptic bats with only modest echolocation and physical differences challenges our understanding of niche partitioning in rhinolophid bats and suggests the possibility that a novel mode of niche partitioning may be used. Alternatively, their distributions may have only recently intersected as a result of forest loss, especially in the lowlands.