Populations of Australian diamondback moth (DBM) Plutella xylostella (L.), a serious pest of cruciferous crops, display extremely low levels of genetic differentiation across Australia and New Zealand sample locations, as determined previously using microsatellite markers. These data suggest high levels of contemporary gene flow that is consistent with Australian DBM being a vagile species. Here we examine Australian DBM samples for haplotype variation using the mitochondrial DNA sequences of a 257 bp fragment of the CO1 gene. We compare this variation to equivalent mtDNA sequence variation in samples from New Zealand, Kenya and Korea. Using 42 moths collected throughout Australia we show that Australian DBM have both low mtDNA haplotype and nucleotide diversities. The three Australian haplotypes detected are closely related and they cluster with the common haplotype group from Indonesia. In addition the Australian haplotype frequency distribution resembled more that from Indonesia than that from Kenya or Korea. These data are consistent with an original strong Australian/New Zealand founder effect, from a south-easte Asian source, with subsequent continued isolation. In a single season, the frequency of PXMt01, the most common Australian haplotype, was estimated at 15 locations spread across southe Australia and New Zealand using a polymerase chain reaction BiPASA method. The PXMt01 haplotype frequency variation was heterogenous,suggesting a small degree of population isolation that was not detected using microsatellites.Differentiation was not a function of geographical distance. These data suggest transient and sporadic local colonisation events by small numbers of founding females.