The early effects of heat stress on the photosynthesis of symbiotic dinoflagellates (zooxanthellae) within the tissues of a reef-building coral were examined using pulse-amplitude-modulated (PAM) chlorophyll fluorescence and photorespirometry. Exposure of Stylophora pistillata to 33 and 34 °C for 4 h resulted in (1) the development of strong non-photochemical quenching (qN) of the chlorophyll fluorescence signal, (2) marked decreases in photosynthetic oxygen evolution, and (3) decreases in optimal quantum yield (Fv/Fm) of photosystem II (PSII). Quantum yield decreased to a greater extent on the illuminated surfaces of coral branches than on lower (shaded) surfaces, and also when high irradiance intensities were combined with elevated temperature (33 °C as opposed to 28 °C). qN collapsed in heat-stressed samples when quenching analysis was conducted in the absence of oxygen. Collectively, these observations are interpreted as the initiation of photoprotective dissipation of excess absorbed energy as heat (qN) and O2-dependent electron flow through the Mehler-Ascorbate-Peroxidase cycle (MAP-cycle) following the point at which the rate of light-driven electron transport exceeds the capacity of the Calvin cycle. A model for coral bleaching is proposed whereby the primary site of heat damage in S. pistillata is carboxylation within the Calvin cycle, as has been observed during heat damage in higher plants. Damage to PSII and a reduction in Fv/Fm (i.e. photoinhibition) are secondary effects following the overwhelming of photoprotective mechanisms by light. This secondary factor increases the effect of the primary variable, temperature. Potential restrictions of electron flow in heat-stressed zooxanthellae are discussed with respect to Calvin cycle enzymes and the unusual status of the dinoflagellate Rubisco. Significant features of our model are that (1) damage to PSII is not the initial step in the sequence of heat stress in zooxanthellae, and (2) light plays a key secondary role in the initiation of the bleaching phenomena.