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There is considerable interest in the processes that generate genetic divergence in marine species and the spatial and temporal scales over which these processes operate. Shark Bay, a large embayment (13,000 km(2)) on the arid west coast of Australia, has been described as a focal point for genetic divergence in marine species due to its heterogeneous environment. This study represents the first DNA-based analysis of the genetic structure of a marine species with pelagic early life stages (ELS) in this region. Twelve microsatellite loci were used to compare the genetic composition of the teleost Chrysophrys auratus from five areas within Shark Bay, and from near-by shelf waters approximately 250 km to the south. The results suggest that the microsatellite composition of C. auratus is homogeneous across most of Shark Bay and near-by shelf waters. This genetic homogeneity is probably maintained via small amounts of contemporary gene flow, which may reduce the potential for C. auratus to locally adapt to the Shark Bay environment. A weakly differentiated assemblage in Freycinet Estuary in the Western Gulf of Shark Bay provided an important exception to the otherwise homogeneous microsatellite composition of C. auratus in the study area. This weak differentiation probably reflects restrictions to gene flow into and/or out of this site due to the temporal isolation of breeding adults, selective mortality of immigrants and/or the presence of hydrological barriers to larval transport. Each of these factors can be linked to environmental heterogeneity in Shark Bay.