The Australian flat oyster Ostrea angasi is currently being assessed for its potential as a species for culture in New South Wales. It is considered important to determine the population genetic structure of wild stocks among estuaries before translocation of juveniles (spat) for growout in order to avoid possible deleterious effects of hybridisation of genetically divergent stocks (i.e. outbreeding depression). Five estuaries were sampled in southern New South Wales as well as another four from across the natural range of the species in Australia. Sequence analysis of a 594 base pair fragment of the mitochondrial cytochrome oxidase I gene was used to determine the degree of population structuring inferred from pairwise Φ_ST estimates and spatial analysis of molecular variance analysis. The analyses revealed that there is no significant genetic differentiation among the sampled New South Wales estuaries (P > 0.05) and all eastern samples represent a geographically homogeneous population. This essentially removes any potential constraints on broodstock sourcing and spat translocation within this region. Although levels of differentiation among all sites varied, little divergence was evident across the entire range of the sample. Furthermore, the study revealed extremely low levels of divergence between O. angasi and its northern hemisphere congener, O. edulis, raising the possibility that O. angasi may have only recently colonised Australian estuaries.