Coral cover is decreasing worldwide largely as a result of a rise in seawater temperatures that triggers coral bleaching and induces coral mortality. Therefore, understanding coral physiological response to rising ocean temperatures poses a challenge for reef conservation. A central aspect of managing coral reefs under global warming lies in accurate species identification and their potential to withstand thermal stress. Cryptic species, morphologically similar but genetically different, typically harbor distinct physiological variation and will respond differently to climate change. A dominant Caribbean reef builder severely affected by climate change is the Mountainous Star Coral, Orbicella faveolata. A recent study reported quantitative genetic variation in the physiological response to thermal stress in a single population of this species, suggesting that variation within populations will allow these corals to adapt to rising ocean temperatures. However, we reanalyzed the data and found multiple cryptic lineages rather than a single panmictic population, with one of the lineages being not heat-tolerant. Our finding of hidden lineages within a threatened species highlights the varying extinction risks faced by these independently evolving groups.