Rapid acute heat stress assays are increasingly used to assess reef coral heat tolerance and identify resilient corals for research and restoration. However, concerns remain about (1) how representative they are of natural bleaching events, and (2) how reproducible they are in resolving differences in heat tolerance among corals. To address these gaps, we (1) compared rapid assays with an 8-day ‘classic’ bleaching experiment on Acropora pulchra genets (n = 20), and (2) tested and retested rapid assay responses of Acropora cervicornis (n = 85 genets) up to a year apart. In both species, rapid assays revealed a ~ 2.5 °C range in heat tolerance thresholds (Fv/Fm ED50s) among genets, and these thresholds were strongly predictive of individual bleaching responses in the classic bleaching experiment (R = 0.74). Retesting genets with rapid assays showed ED50 differences < 0.99 °C in 90% of cases (median = 0.47 °C), and controlling for environmental effects reduced these to < 0.54 °C (median = 0.23 °C). Even so, large differences (> 0.93 °C) were needed between two individual genets to reliably retest in the same rank order, though smaller margins were reproducible for groups (e.g., 0.29 °C for groups of 10). These results demonstrate that rapid assays may not resolve fine-scale individual heat tolerance differences, but they can easily identify top- and bottom-performing individuals, and differential tolerance between groups of corals. These findings provide critical validation and quantitative guidelines for the use of rapid assays, which may transform coral heat tolerance research and its applications to reef restoration.