Adaptive variation in thermal bleaching tolerance is increasingly recognised as a key aspect for coral ecological persistence. Elucidating conserved phenotypic and molecular signatures of thermal tolerance across local and regional scales is needed to advance our understanding of adaptive variation and remains largely unresolved. This is due to a lack of standardized experimental frameworks and studies aligning phenotype characteristics with underlying genetic makeup of coral genotypes. Acute heat stress assays (Maximum Monthly Mean +9oC) are predictive of the bleaching phenotype and can be standardised across a large number of species, sites and regions within a cross-comparable timeframe. Here we present results derived from this approach, which identifies thermal tolerance variation within populations of four Great Barrier Reef (GBR) species across multiple sites spanning a latitudinal gradient. Effective Dose 50 (ED50- 50% decline in photosynthetic efficiency) determination is used as a metric of coral thermal tolerance, showing a consistent response within species across sites and a strong positive relationship to visual bleaching scores and host protein across all taxa. Analysis of the ITS2 region resolves distinct differences in the algal symbiont composition among species across sites. These measures are thus predictive of among and within species bleaching variation and findings will contribute to the development of resilience biomarkers and inform management and restoration actions at local and regional scales.