Thermal anomalies caused by climate change are increasing in frequency and intensity causing widespread coral bleaching. This process is complex and varies among coral colonies across spatial and temporal scales. Naturally temperature tolerant genotypes may hold the key to adaptation to temperature anomalies, however, we have a poor understanding of where these individuals occur and the underlying mechanisms of thermal tolerance. Current knowledge based on predictive modelling and remote observations lack the spatial resolution required to detect variation at smaller scales such as among genotypes. To address this knowledge gap, we tagged 350 Acropora millepora colonies across 4 reefs within Woppaburra sea Country (Keppel Islands). Colonies varied in bleaching response in April 2020 but most recovered with ~94% of tagged colonies fully pigmented by October 2020. We exposed these colonies to a rapid heat stress assay and used PAM chlorophyll fluorescence to determine photosynthetic efficiency and hyperspectral imaging to measure photo pigment. By comparing these results to the natural bleaching data, we benchmark the novel and high throughput acute heat stress approach. This method will enable us to rapidly identify thermally tolerant genotypes in large sample sizes across environmental gradients to increase our understanding of adaptive variation across reef scapes.