Physiological performance of marine fishes is highly sensitive to changes in temperature, such that spatial and temporal variation in ocean temperatures may have a marked impact on activity and behaviour. This study uses acoustic telemetry to examine variation in habitat use of coral trout (Plectropomus leopardus) among seasons and between locations in the northern versus southern sectors of the Great Barrier Reef, Australia. Spatial and temporal differences in habitat use were strongly linked to seasonal and latitudinal variation in temperature. The southern population typically had larger home ranges than the northern population, 0.29 km2 compared to 0.23 km2 respectively and space use decreased substantially during the summer time, particularly for the northern population. This study provides important information on the effects of increasing temperature on fine-scale movements and habitat use of wild stocks of coral trout. These data complement existing tank based studies, to better inform predictions about how P. leopardus populations and coral reef fisheries generally, might be impacted by sustained and ongoing global climate change.