The difference in stress response between coral species that are resistant (Montipora capitata) and susceptible (Pocillopora acuta) to changes in environmental conditions can be used to better understanding coral resilience to anthropogenic climate change. Over a 16-week period, coral nubbins from two species were exposed to one of four conditions: Ambient Temperature Ambient CO2, Ambient Temperature High CO2, High Temperature Ambient CO2, or High Temperature High CO2. Multi-omics, including meta-transcriptome, data were generated at various time points during the experiment.