Allozyme electrophoresis and mitochondrial DNA sequences were used to assess genetic variation in a small macropod marsupial, the quokka (Setonix brachyurus). Setonix brachyurus is restricted to the southwest corner of Western Australia. Its habitat has been fragmented at least since the late Pleistocene by rising sea levels, creating two island populations, and more recently through anthropomorphic modification of the mainland habitat. Genetic analyses showed low levels of variation for allozymes (two polymorphic loci), although there was significant heterogeneity among populations (overall FST=0.362). Nucleotide sequence diversity was low (π=0.028) while haplotype diversity was high (H=1.0). Overall, the patterns of genetic variation reflect a shallow history, but with restricted gene flow across the species' range.