Populations established on the Eyre Peninsula and Kangaroo Is. have expanded rapidly to reach carrying capacity, and in the latter case now number several thousand individuals. This situation may have resulted in the perception that loss of genetic variation and fitness, which could occur as a consequence of severe bottlenecks or of founding events (Wright, 1931, 1969), does not ultimately pose a serious threat to these koalas’ longterm survival. In this study we used microsatellite markers, which have proved to be sensitive measures of genetic variation in the koala (Houlden et al., 1996), to quantify levels of genetic variation within the South Australian koala populations and the relatively unperturbed Strzelecki Ranges population from Victoria. We also quantified differentiation between these populations and French Is., using microsatellites and mtDNA d-loop region variation (Houlden et al., 1999). Finally, we investigated rates of physical abnormalities present in these highly inbred populations relative to the unperturbed Pilliga State Forest population (Montgomery, 2001) which may indicate inbreeding depression is occurring in koalas.