Significance Although climate change is expected to decimate coral reefs, the combined impacts of ocean-warming and acidification on coral reef biodiversity remains largely unmeasured. Here, we present a two-year mesocosm experiment to simulate future ocean acidification and ocean-warming to quantify the impacts on species richness, community composition, and community structure. We find that species richness is equivalent between the dual-stressor and present-day treatments but that the community shuffles, undoubtedly altering ecosystem function. However, our ability to predict the outcomes of such community shuffling remains limited due to the critical knowledge gap regarding ecological functions, life histories, and distributions for most members of the cryptobenthic community that account for the majority of the biodiversity within these iconic ecosystems.