Studies of the regulation and importance of physiological processes such as coral photosynthesis and respiration on coral reefs require knowledge of spatio-temporal patterns of variability at different scales. Oxygen microelectrodes were used to measure photosynthesis and dark respiration of 2 corals, Pocillopora damicornis and Turbinaria reniformis, in the northern (Lizard Island) and central (Davies and Broadhurst Reefs) regions of the Great Barrier Reef (GBR) in winter and summer. Genetic characterisation of Symbiodinium revealed that P. damicornis hosted a single symbiont type (Symbiodinium C1) in both regions, whereas T. reniformis harboured 2 types, dependent on location. Colonies at Lizard Island harboured Symbiodinium D, whereas colonies at Davies Reef harboured Symbiodinium C2. Rates of gross photosynthesis were greater in the central than in the northern GBR in summer. A similar pattern was detected for dark respiration rates in T. reniformis. No seasonal change in either photosynthesis or dark respiration was evident in the northern GBR, possibly due to less annual variability in light conditions, and for T. reniformis, additionally the presence of Symbiodinium D. These results highlight that environmental conditions coupled with regional-scale distribution of Symbiodinium are likely to exert important influences on respiration and photosynthetic performance of reef-building corals.