Photoacclimation of the symbiotic hermatypic coral Stylophora pistillata was studied both for colonies growing at different depths (1 to 20 m) sampled within the same season ('spatial photoacclimation') and for colonies growing at the same depth (5 m) but sampled throughout the year ('temporal photoacclimation'). Specimens were darker and had increased chlorophyll densities (chlorophyll per coral surface area) under low-light conditions caused both by increased depth and, in shallow-growing specimens, by the winter season. However, while increased depth involved increased zooxanthella chlorophyll content, acclimation to low irradiances by shallow-growing corals during the winter mostly involved an increase in algal density. In shallow-growing corals, both zooxanthella chlorophyll content and coral chlorophyll density fluctuated seasonally in correlation with light more than with nitrogen or temperature. This could be related to the fact that reefs in Eilat, Israel, are exposed to more solar radiation than many other reefs in the world. Histological analyses of high-light corals showed that zooxanthellae were located deeper inside the host tissue and were smaller in diameter compared to zooxanthellae from low-light corals. Additionally, while deep-water colonies hosted clade C zooxanthellae, colonies growing in shallow waters, both in high-and very low-light environments, hosted clade A. These clade differences were found to affect coral physiology, as examined in a short-term thermal stress experiment, with clade-A colonies having higher thermal resilience than clade-C colonies. Taken together, our results show evidence of different mechanisms that help adjust the light-capturing abilities of S. pistillata zooxanthellae to spatial and temporal changes in irradiance.