Rising CO2 levels in the sea threaten to break-down the important relationship between reef-building corals and their symbiotic dinoflagellates. Photorespiration plays a significant role in maintaining dinoflagellate well-being by offering an alternative photochemical-quenching pathway and potentially triggering the Carbon-Concentrating Mechanism. As photorespiration is dependant on the ratio of CO2 to O2, rising CO2 may ultimately lead to reduced capacity for photoprotection and increased occurrence of coral bleaching. Here we present data from a microcosm experiment with controlled levels of CO2 and O2. Physiological data has been derived from classical respiration measurements to produce Photosynthesis-Irradiance (P-E) curves. The P-E curves showed a decline in symbiont production at the highest CO2 level (1100 ppm, pH 7.6). Excitation pressure, measured with a pulse amplitude modulation fluorometer, increased significantly with increasing CO2 and decreasing O2. However, these relationships were dependant on the proximity of growth light to saturating light intensities. We observed calcification at pH 7.8 but decalcification at pH 7.6 using the total alkalinity technique. These findings were closely linked to the gene expression of a key enzyme in the photorespiratory pathway, phosphoglycolate phosphatase (PGPase). mRNA of PGPase declined significantly by 54% at 560 ppm CO2 (pH 7.8) and by 70% at 1100 ppm CO2 (pH 7.6). This decline in photorespiration at high CO2 provides a key insight towards the mechanism of CO2-induced bleaching.