Although pademelons (Thylogale) are widespread and common in coastal eastern Australia, they have been largely neglected in population genetic studies. Here we use 10 microsatellite loci and the mitochondrial DNA (mtDNA) cytochrome b (Cytb) gene to examine genetic differentiation amongst populations of the red-necked (Thylogale thetis) and red-legged (T. stigmatica) pademelon in eastern Australia. Evidence of hybridisation was detected between subspecies of T. stigmatica in central Queensland. Specimens sampled between Eungella and Sarina were found to represent a broad (~90 km) zone of introgression, for both nuclear and mtDNA markers, between T. s. stigmatica (Wet Tropics) and T. s. wilcoxi (south-east Queensland). In addition, individuals sampled from around Proserpine were genetically T. s. stigmatica rather than T. s. wilcoxi, as had previously been assumed. This observation raises some intriguing questions about the dispersal ability of T. stigmatica and the phylogeographic history of moist forest taxa in eastern Australia. Only limited evidence of introgression was detected between sympatric populations of T. thetis and T. s. wilcoxi in south-east Queensland.