Anthropogenic climate change has caused widespread loss of species biodiversity and ecosystem productivity globally. Coral reef ecosystems have proven particularly susceptible to heat stress. Hence, predicting future vulnerability of reef-building corals is crucial for cost-effective conservation planning. In this study, we combine regional population genetic connectivity and seascape analyses to explore genetic offset patterns (mismatch of gene-environmental associations under future climate conditions), in a reef-building coral across northwest Australia. Our data revealed limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified loci strongly associated with the regional temperature variation, which were used to forecast future genetic offset using a random forest model. Our model identified pronounced differences in the response of different reef systems in Western Australia to predicted increasing temperatures. Under the extreme climate scenario (RCP 8.5), all reef systems are predicted to experience a large gene-environment disconnect, and show extensive mismatch between current allele frequencies and those required to cope with local environmental change. The results here suggest complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing for coral reef resilience into the future.