Small increases in ocean temperature can resulting in coral bleaching. Coral bleaching is the loss of algal symbionts from the coral host. Little is known about the genes that drive the bleaching of algal symbionts under elevated temperature. Here we compare gene expression between a strain of symbiotic algae compared with an experimentally evolved strain to elevated temperature over 80 generations. Genes found to be involved in thermal tolerance could be targeted to develop thermally resilient algal symbionts for use in coral restoration and conservation initiatives.