Mud crabs (Portunidae; Scylla spp.) have become established recently in some south-west Australian estuaries - almost 1000 km south of their recorded distribution. Colonisation may have occurred by a natural range expansion from the north-west or by translocation from source(s) within the Indo-West Pacific. To identify the species and the potential source population(s), genetic analyses was used to compare south-west crabs (N = 32) to other populations. Levels of diversity at two independent genetic markers were also compared to obtain relative estimates of effective population size between colonist and suspected source population(s). Comparisons of mitochondrial DNA sequences (COI) indicated that all south-west crabs were Scylla serrata. Indeed, the sole haplotype found among colonists was identical to one prevalent but endemic to more diverse north-west Australian populations. In contrast, source and colonist populations had equally high levels of genetic diversity at two microsatellite loci. It is argued that the south-west region was colonised by large numbers of S. serrata from north-west Australia through a recruitment event enhanced by the strong 1999/2000 Leeuwin Current. Differences in diversity among nuclear and mitochondrial loci may reflect different responses to the colonisation process; it is predicted that such differences are prevalent among plankton-dispersed species.