Increased ocean temperatures are thought to be triggering mass coral bleaching events around the world. The intracellular symbiotic zooxanthellae (genus Symbiodinium) are expelled from the coral host, which is believed to be a response to photosynthetic damage within these symbionts. Several sites of impact have been proposed, and here we probe the functional heterogeneity of Photosystem II (PSII) in three coral species exposed to bleaching conditions. As length of exposure to bleaching conditions (32°C and 350 μmol photons m⁻² s⁻¹) increased, the Q_A⁻ reoxidation kinetics showed a rise in the proportion of inactive PSII centers (PSII_X), where Q_B was unable to accept electrons. PSII_X contributed up to 20% of the total PSII centers in Pocillopora damicornis, 35% in Acropora nobilis and 14% in Cyphastrea serailia. Changes in F_v/F_m and amplitude of the J step along fast induction curves were found to be highly dependent upon the proportion of PSII_X centers within the total pool of PSII reaction centers. Determination of PSII antenna size revealed that under control conditions in the three coral species up to 60% of PSII centers were lacking peripheral light-harvesting complexes (PSIIβ). In P. damicornis, the proportion of PSIIβ increased under bleaching conditions and this could be a photoprotective mechanism in response to excess light. The rapid increases in PSII_X and PSIIβ observed in these corals under bleaching conditions indicates these physiological processes are involved in the initial photochemical damage to zooxanthellae.