Corals today face increasingly challenging conditions, including rising ocean temperatures brought about by climate change. To gain insight into how phylogenetically divergent species may respond to thermal stress events, we compared the gene complement of four coral species, Acropora digitifera, Favites colemani, Montipora digitata, and Seriatopora caliendrum, that were previously shown to have different sensitivities to acute thermal stress. Comparison of gene repertoires in the four scleractinian corals revealed an extensive set of cnidarian stress response genes (SRGs). Antioxidant protein families and chaperones were relatively more abundant in F. colemani and M. digitata, proteins linked to immunological functions were enriched in S. caliendrum and A. digitifera, and extracellular matrix components were abundant in S. caliendrum and F. colemani. The species that showed greatest heat susceptibility, S. caliendrum, also exhibited drastic upregulation of SRGs under acute thermal stress. This suggests that differences in SRG complement, as well as the mechanisms that control SRG expression response, contribute to the ability of corals to maintain stable physiological functions and to survive shifts in seawater temperature.