Continuous pulse amplitude-modulated (PAM) fluorescence measurements were performed in situ under natural irradiances for colonies of the coral Stylophora pistillata growing in shallow (2 m) and deeper (11 m) waters of the Red Sea. The effective quantum yield (ΔF/F′m) showed a diurnal pattern inversely related to that of the incident downwelling photosynthetically available radiation (PAR), but this pattern was skewed for the shallow colonies such that the values were always lower in the afternoon than during morning hours when measured at similar irradiances. Accordingly, the relative photosynthetic electron transport rate (rETR, = ΔF/F′m X incident PAR) for those colonies also showed lower values in the afternoons than in the mornings at equal irradiances. The rETRs also saturated well before maximal midday irradiances occurred. At the same time, nonphotochemical quenching (NPQ, measured as [Fm - F′m]/F′m) was higher in the afternoons than during the mornings under similar incident PAR values. These results indicate an afternoon loss in photosynthetic capacity from photoinhibition. Such photoinhibition was not apparent during the course of the day in the corals growing in deeper water. The latter also showed no saturation of photosynthesis at the highest incident PAR values at noon (which were approximately a third of those at the shallower site). In addition, the shallow-growing corals showed significantly lower maximum quantum Yields (ΔF/F′m measured during nighttime, equivalent to Fv/Fm) than the deeper growing ones. This is most likely caused by an additional, more chronic, photoinhibition in the shallow-growing corals but could also be due to some form of photoacclimation or to factors other than light.