The red sea urchin Mesocentrotus franciscanus is an ecologically important kelp forest herbivore and an economically valuable fishery species. To examine of how M. franciscanus responds to its environment on a molecular level, differences in gene expression patterns were observed in embryos raised under combinations of two temperatures (13C and 17C) and two pCO2 levels (475 uatm and 1050 uatm). The transcriptomic responses of the embryos were assessed at two developmental stages (gastrula and prism) in light of previously described plasticity in body size and thermotolerance under these temperature and pCO2 treatments. Although transcriptomic patterns primarily varied by developmental stage, there were pronounced differences in gene expression as a result of the treatment conditions. Temperature and pCO2 treatments led to the differential expression of genes related to the cellular stress response, transmembrane transport, metabolic processes, and the regulation of gene expression. Temperature had a greater influence on gene expression than pCO2, and may have contributed to positive effects of temperature on body size and thermotolerance at the prism stage. On the other hand, a relatively muted transcriptomic response to pCO2 may have permitted the stunting effect of elevated pCO2 on embryo body size. M. franciscanus exhibited both transcriptomic and phenotypic plasticity in response to temperature and pCO2 stress during early development. As climate change continues, red sea urchins may benefit from moderate ocean warming, whereas they will be negatively affected by ocean acidification. Present-day pCO2 conditions that occur due to coastal upwelling may already be detrimental to populations of M. franciscanus.