Sessile, long-lived organisms such as reef-building corals are particularly vulnerable to the rapid environmental shifts caused by climate change. Phenotypic plasticity plays an important role in the ability of these organisms to persist in a changing environment, and is often mediated through changes in gene expression. Here, we use genome-wide gene expression profiling to explore genotype-level differences in the response to combined thermal and ocean acidification stress, both individually and combined, in the threatened Caribbean coral Acropora cervicornis.