Significance Coral reefs are biodiversity hotspots of great ecological, economic, and aesthetic importance. Their global decline under climate change and other stresses makes it urgent to understand the molecular bases of their responses to stress, including “bleaching,” in which the corals' photosynthetic algal symbionts are lost, thus depriving the host animals of a crucial source of energy and metabolic building blocks. We sought clues to the mechanisms that cause (or protect against) bleaching by analyzing the patterns of gene expression in a sea anemone relative of corals during exposure to a heat stress sufficient to induce bleaching. The results challenge some current ideas about bleaching while also suggesting hypotheses and identifying genes that are prime targets for future genetic analyses.