In the family Rhinolophidae, the members of the trifoliatus clade are easily recognisable by a unique noseleaf structure and a fluffy fur. Within this group, Rhinolophus luctus is the largest species with currently six recognized subspecies, distributed from India to Bali. We investigated genetic (karyotype, mitochondrial DNA sequence) and morphological characters from a Peninsular Malaysian sample. Although the diploid number was 2n = 32 in all specimens, karyotype analysis revealed two largely different chromosomal sets, with a Y-autosome translocation present only in one of the taxa. Morphological examination revealed differences concerning size of the baculum and length of the lower toothrow. Based on these results, a new species is described and the former subspecies distributed on the Malayan Peninsula, Rhinolophus luctus morio, is elevated to species rank, Rhinolophus morio.