It is increasingly recognised that intertaxon hybridisation is more common in vertebrates than previously thought. However, recent hybridisation has rarely been reported from wild marsupials, with only three instances of first generation (F1) hybrids reported, all in macropodids. In the 1990s a chromosomally anomalous population of black-footed rock-wallaby (Petrogale lateralis) was identified in the Townsend Ridges in central eastern Western Australia. Individuals from this population had chromosomes characteristic of two P. lateralis subspecies (P. l. centralis and P. l. kimberleyensis). This unusual mixture is suggestive of a novel hybrid zone between subspecies, but it could also represent a P. l. centralis population in which a 9–10 chromosome fusion has independently arisen. To test between these hypotheses, we compared mitochondrial DNA Control Region (CR) sequence data from Townsend Ridges individuals to published data for all P. lateralis subspecies. Two divergent lineages of CR haplotypes were identified at Townsend Ridges, suggesting that it represents a novel rock-wallaby hybrid zone, the third reported in the genus. While one CR haplotype clustered with those typical of P. l. centralis, the other Townsend Ridges haplotypes clustered with those from three different P. lateralis subspecies but not with P. l. kimberleyensis. Additional studies with multiple nuclear genes will be necessary to fully understand the nature of this novel hybrid zone.