Coral bleaching is now the main driver of reef degradation. The common notion is that most corals bleach and suffer mortality at just 1-2°C above their mean summer maximum temperatures, but some species and genotypes resist or recover better than others. Here we conducted a series of 18-hour short-term heat stress assays side-by-side with a long-term heat stress experiment to assess the ability of both approaches to resolve putative differences in coral thermotolerance and provide a measure of in situ reef temperature thresholds. Using a suite of measures (photosynthetic performance, coral whitening, chlorophyll a, host protein, algal symbiont counts, and algal type association), we assessed bleaching sensitivity/resilience of Stylophora pistillata colonies from the exposed and protected sides of a near-shore coral reef in the central Red Sea. As suggested by the differential mortality during a previous bleaching event, coral colonies from the protected site exhibited less impacted physiological performance in comparison to their exposed site counterparts, and these differences were resolved using both experimental setups. Notably, the long-term experiment provided better resolution with regard to the different measures collected, but at the price of portability, cost, and duration of the experiment. Variability in resilience to ocean warming is critical to reef persistence, yet we lack standardized diagnostics to rapidly assess bleaching severity or resilience across different corals and locations. Using a newly developed portable experimental system termed CBASS (the Coral Bleaching Automated Stress System), we demonstrate that mobile, short-term heat stress assays can resolve fine-scale differences in coral thermotolerance across reef sites. Based on our results, photosynthetic efficiency measured by non-invasive PAM fluorometry provides a rapid and representative proxy of coral resilience. Our system holds the potential to be employed for large-scale determination of in situ bleaching temperature thresholds across reef sites and species. Such data can then be used to identify resistant genotypes (and reefs) for downstream experimental examination and to complement existing remote-sensing approaches.