Marine ecosystems face increasing threats from rising global temperatures and intensified disturbance regimes. Coral reefs are no exception and are facing rapid declines globally. Characterising the key parameters that drive resilience to recurrent heat stress has never been so pertinent. In this study, we characterised patterns of spatial genetic structure and connectivity, symbiont community dynamics, and heat tolerance in corals from three distinct bioregions of the World Heritage Ningaloo Reef Marine Park by combining low-coverage whole genome re-sequencing, ITS2 metabarcoding, and acute experimental heat stress assays. Whole genome data revealed strong isolation of Ningaloo Reef from offshore oceanic reef systems in Western Australia, and limited connectivity between regions within the Ningaloo Reef Marine Park. Despite this restricted gene flow, corals harboured similar symbiont communities and showed a similar response to acute heat stress. This research provides insights into the adaptive capacity of Ningaloo by employing a suite of targeted tools to understand climate resilience, supporting conservation management amid escalating climate challenges.