This study tested the bleaching response of the Pacific coral Seriatopora caliendrum to short-term exposure to high temperature and elevated partial pressure of carbon dioxide (pCO2). Juvenile colonies collected from Nanwan Bay, Taiwan, were used in a factorial experimental design in which 2 temperatures (∼27.6 7C and ∼30.4 7C) and 2 pCO2 values (∼47.2 Pa and ∼90.7 Pa) were crossed to evaluate, over 12 days, the effects on the densities and physiology of the symbiotic dinoflagellates (Symbiodinium) in the corals. Thermal bleaching, as defined by a reduction of Symbiodinium densities at high temperature, was unaffected by high pCO2. The division, or mitotic index (MI), of Symbiodinium remaining in thermally bleached corals was about 35% lower than in control colonies, but they contained about 53% more chlorophyll. Bleaching was highly variable among colonies, but the differences were unrelated to MI or pigment content of Symbiodinium remaining in the coral host. At the end of the study, all of the corals contained clade C Symbiodinium (either C1d or C15), and the genetic variation of symbionts did not account for among-colony bleaching differences. These results showed that high temperature causes coral bleaching independent of pCO2, and underscores the potential role of the coral host in driving intraspecific variation in coral bleaching.