There are a wide variety of fishes that occur exclusively on coral reefs, though it is unclear to what extent these species (especially larger-bodied fisheries target species) are reliant on the specific reef habitat provided by corals. This study explored variation in the physiological condition of common coral trout (Plecropomus leopardus) on Australia’s Great Barrier Reef, explicitly testing whether fish condition varied with local coral cover in the aftermath of severe mass bleaching and coral loss. Both the physiological condition (specifically, the length–weight relationships, hepatocyte vacuolation, and electrical phase angle) of P. leopardus and the live cover of habitat-forming corals varied greatly among the sites considered in this study, but there was little correspondence between these factors. Fish condition was largely influenced by fish size and varied with latitude. While there was no apparent effect of recent coral bleaching and coral loss on the physiological condition of P. leopardus, this does not mean that these key fisheries species will be unaffected by further changes to the environmental conditions and reef habitat. It is important, therefore, that fisheries managers remain vigilant to apparent effects of climate change and other anthropogenic pressures on fisheries stocks.