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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 (F_v/F_m) 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 …