Genotyping of koalas at CA-repeat microsatellite loci has revealed significant differences in the levels of allelic diversity (A) and expected heterozygosity (HE) between populations from north-eastern and south-eastern Australia. In the 10 populations studied, allelic diversity ranged from 8.0 in the Nowendoc population to 1.7 in the Kangaroo Is. population, and values of HE ranged from 0.831 in the Nowendoc population to 0.331 in the Kangaroo Is. population. Data from pooled populations revealed koalas from the northeastern region had significantly higher levels of allelic diversity (A= 11.5 ± 1.4) than those from south-eastern Australia (A= 5.3 ± 1.0). Furthermore significantly higher heterozygosity levels were found in the north-eastern (HE= 0.851) vs. the south-eastern (HE= 0.436) regions of Australia. Following a near-extinction bottleneck in the 1920s, mainland Victorian and Kangaroo Is. koalas have been involved in an extensive program of relocations. The source populations of the relocated animals were islands in Westernport Bay, which were founded by very few individuals in the late 1800s and early 1900s. The significantly lower levels of variation between south-eastern Australian populations suggests that human intervention has had a severe effect on levels of genetic diversity in this region, and this may have long-term genetic consequences.