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Climate change is resulting in warmer temperatures that are negatively impacting corals. Understanding how much individuals within a population vary in their thermal tolerance and whether this variation is heritable is important in determining whether a species can adapt to climate change. To address this, Acropora cervicornis fragments from 20 genetically distinct colonies collected from the Coral Restoration Foundation Tavernier nursery (Florida, USA) were kept at either ambient (28 ± 1°C) or elevated (32 ± 1°C) temperatures, and mortality was monitored for 26 d. Both broad-sense ( H 2 ) and narrow-sense ( h 2 ) heritability of thermal tolerance were estimated to determine the amount of genetic variation underlying survival to elevated temperature. To understand the physiological basis of thermal tolerance, tissue from both treatments was taken 12 h after the start of the experiment to investigate gene expression at the mRNA and protein level between tolerant and susceptible colonies. Results revealed that this population has considerable total genetic variation in thermal tolerance ( H 2 = 0.528), but low variance in relatedness among colonies prevented us from making any conclusions regarding h 2 . Despite high transcriptomic variability among and within colonies, 40 genes were consistently and significantly different between tolerant and susceptible colonies, and could be potential biomarkers for thermal tolerance should they be verified in a larger sample. Overall, the results suggest that this population has substantial genetic variation for traits that directly impact thermal tolerance; however, their response to projected increases in temperature will depend on more precise estimates of the additive components of this variation ( h 2 ).