To examine whether damage to zooxanthellar photosystem II (PSII) is the primary step of thermally induced coral bleaching, we first assessed the relationship between the maximum quantum yield of PSII (F_v/F_m) or active PSII centers (F_v/F_o) and maximum electron transport rate (ETR_max), which represent the PSII activity and electron flow beyond the PSII, respectively, in the symbiotic algae of the coral Pachyseris rugosa. Next, the photo-physiological responses of the symbionts to stress treatments of 1h high temperature (33.5°C) and/or high light (1030μmol quanta m^-2 s^-1) stress and 6h recovery were investigated. The 1h high temperature treatment in darkness produced a significant, but reversible (6h recovery) decline in ETR_max without any change in F_v/F_m. The 1h high light treatment reduced F_v/F_m, but not ETR_max. High temperature in combination with high light resulted in a more pronounced reduction in F_v/F_m, along with a significant decline in ETR_max. Neither F_v/F_m nor ETR_max recovered fully within 6h. Reversible increases in non-photochemical quenching (NPQ), energy dissipation in PSII, were also recorded. Chloramphenicol (CAP), an inhibitor of synthesis of D1 protein of PSII reaction center, revealed that a minimum of -60% of the F_v/F_m or -30% of active PSII centers (F_v/F_o) is required to maintain ETR_max in the in hospite symbionts. These results suggest that the primary step of heat-induced damage in the symbiont's photosynthetic apparatus involves a component beyond the PSII, probably at the level of the dark reaction as indicated by reduced ETR_max and the PSII damage is secondary.