The four endemic species of rock-wallabies (P. brachyotis, P. burbidgei, P. concinna, P. wilkinsi) from north-west Australia represent a monophyletic lineage within Petrogale that diverged early in the evolution of the genus. Preliminary mitochondrial DNA (mtDNA) studies have revealed high levels of divergence and/or a lack of monophyly within most species. However, improved resolution was impeded by a lack of high quality genetic samples from key areas and taxa, as well as the examination of small numbers of loci. This study used next generation sequencing methods (targeted exon capture) to sample > 1,000 loci from across the genome of the 4 species of rock-wallabies from north-western Australia, and enabled museum skins to be utilised as a source of DNA. Analysis of the nDNA data reveals more divergent, well supported monophyletic lineages than the 4 currently recognised species in this group, indicating that additional taxonomic revision is required. The mtDNA reveals a complex and discordant pattern of relationships that appears the result of ancient hybridisation and introgression