Coral trout (genus Plectropomus) are a group of iconic predatory reef fishes and represent important commercial and recreational fisheries in Australia’s tropics. The common coral trout, P. leopardus, are abundant through the Great Barrier Reef and occur on several remote atolls in the Australian Coral Sea Marine Park. Studying how these populations are connected is crucial for defining management units, implementing effective marine reserves and understanding the resilience of remote populations through time.  This study used modern genomic techniques to test for patterns of population structure among P. leopardus on the Great Barrier Reef and the Coral Sea. Genetic structure was compared to regional oceanic currents to investigate the influence of environment on dispersal and connectivity. Patterns of selection were also compared between populations to test for signatures of localised adaptation.