Given the threats of greenhouse gas emissions and a changing climate to marine ecosystems, there is an urgent need to better understand the response of not only adult corals, which are particularly sensitive to environmental changes, but also their larvae, whose mechanisms of acclimation to both temperature increases and ocean acidification are not well understood. Brooded larvae from the reef coral Pocillopora damicornis collected from Nanwan Bay, Southern Taiwan, were exposed to ambient or elevated temperature (25 or 29 oC) and pCO2 (415 or 635 matm) in a factorial experiment for 9 days, and a variety of physiological and molecular parameters were measured. Respiration and rubisco protein expression decreased in larvae exposed to elevated temperature, while those incubated at high pCO2 were larger in size. Collectively, these findings highlight the complex metabolic and molecular responses of this life history stage and the need to integrate our understanding across multiple levels of biological organization. Our results also suggest that for this pocilloporid larval life stage, the impacts of elevated temperature are likely a greater threat under near-future predictions for climate change than ocean acidification.