Craseonycteris thonglongyai (Chiroptera: Craseonycteridae), an enigmatic taxon which shares morphological traits with both Rhinopomatidae and Emballonuridae was for the first time investigated with the aid of molecular phylogenetic techniques. Three methods of phylogenetic inference, parsimony, maximum-likelihood, and Bayesian phylogenetics were used. Based on 402 bp of DNA sequence from the mitochondrial cytochrome b gene, placement of Craseonycteridae within the superfamily Rhinolophoidea was demonstrated. Our results also suggest close proximity of Craseonycteridae to Hipposideridae rather than to Rhinopomatidae, close relationships between Megadermatidae and Rhinolophidae, sister group position of Pteropodidae to Rhinolophoidea, and closer affiliation of Nycteridae with the infraorder Yangochiroptera. Spectral analysis was in agreement with all these outcomes except for closer relationships of Craseonycteris with Rhinopomatidae.