Many rock-wallaby (Pestrogale) species within the lateralis - Penicillata complex are morphologically similar and can be distinguished only by their unique karyotypes, frustrating attempts to identify specimens in the field and in museums. As chromosome preparations are not always obtainable from specimens, additional diagnostic molecular markers are required. In this study, restriction fragment length polymorphism (RFLP) analysis of three nuclear genes was undertaken using 100 Petrogale specimens, including representatives of 12 taxa. Eleven novel diagnostic nuclear DNA markers were identified, which enabled the identification of four taxa (P. penicillata, P. purpureicollis, P. lateralis and P inornata). No markers were found that could reliably distinguish amongst five north-east Queensland species (P. assimilis, P. sharmani, P. mareeba, P. godmani and P. coenensis) or the sampled intraspecific taxa of P. lateralis (P. I. lateralis, P. I. pearsoni, MacDonnell Ranges race). These results are consistent with previous studies in demonstrating that P. penicillata, R purpureicollis, P. lateralis and P. inornata are genically distinct and that the north-east Queensland species and subspecies/races of P. lateralis form two groups of very closely related taxa. Future research should target more rapidly evolving DNA regions, in order to identify specific molecular markers that distinguish amongst taxa within these two groups. Meanwhile, karyotypic analysis remains the only definitive technique currently available to unambiguously identify all taxa within the lateralis - Penicillata group.