Past taxonomic studies of cockroaches in the genus Paratemnopteryx Saussure (Blattodea: Blattellidae) indicate the presence of different races of P. stonei Roth from cave populations in northeastern Australia. Morphometric analyses were carried out to investigate the morphological variation among individuals from four cave regions, including representatives of each of the races previously noted. Published canonical discriminant analyses, and additional cluster analyses, presented in this article, indicate morphological discontinuities among the populations. In addition, specimens collected from one region, although morphologically similar to P. stonei, are regarded as representing a new species of Paratemnopteryx. To investigate the utility of molecular data at the population and species level for this genus, we sequenced the second internal transcribed spacer (ITS2) region of nuclear ribosomal DNA. Sequences were obtained from 14 individual cockroaches used in the morphometric analyses. The size of the ITS2 gene region was 504–592 bp, with a mean G C content of 52.3%. We found that the ITS2 data supported the existence of at least three races of P. stonei, and the new species of Paratemnopteryx. We concluded that the ITS2 region is useful for taxonomic discrimination at the population and species level within Paratemnopteryx, and can help throw light on the evolution of cave dwelling species.