Genetic identification of individual animals from remotely collected DNA samples provides an alternative approach for the collection of data on populations of elusive or rare species. In this study we used DNA isolated from field-collected faecal samples to estimate the size of a population of common wombats (Vombatus ursinus) surviving in suburban Melbourne parkland. A pilot study revealed that microsatellite genotypes obtained from DNA in faeces were often incorrect, but that by carrying out three replicate polymerase chain reactions (PCRs) for each sample, we were able to reliably identify individuals. We conducted a mark-recapture study using the Mh-jackknife model to estimate the size of the wombat population at Mt Lofty Reserve, and identified 17 individuals - 10 males and seven females. The interpolated population size estimate was 19 with a 95% confidence interval of 18-32. The distribution of individual wombats' scats provided information on ranging behaviour. The genotypic database obtained was used to identify five of the individuals as putative immigrants, suggesting that the population is not isolated from others in a series of reserves along the Yarra River. However, the lack of a detectable female bias in immigration differs from our previous findings in continuous populations of this species. The level of genetic variation at the five loci analysed was also inconsistent with long-term isolation of the population.