Coral bleaching is the manifestation of the dysfunction of the symbiosis between scleractinian corals and dinoflagellates of the diverse genus Symbiodinium and is induced by elevated temperatures and high irradiance. We investigated the photophysiological response of two genetically distinct Symbiodinium subtypes within clade A upon exposure to elevated temperatures at two light intensities for 3 weeks. While both subtypes displayed a characteristic photoacclimation to high light (HL) (decrease in light-harvesting pigments, lower photochemical efficiency of photosystem II, increased xanthophyll pool sizes), the tolerance toward thermal stress clearly differed between the two subtypes. Symbiodinium Ax was highly susceptible to chronic photoinhibition at temperatures ≥30°C, which was exacerbated under HL conditions. A1 showed a capacity for photoacclimation and high thermal tolerance, which might be related to higher cellular concentrations of photoprotective xanthophylls and the low-molecular antioxidant glutathione (GSx) along with the dynamic regulation of these photoprotective pathways. Whereas HL conditions induced both accumulation of diatoxanthin and GSx, thermal stress further stimulated xanthophyll cycling, which might compensate for diminished amounts of GSx at elevated temperatures. Our results show that the two clade A subtypes clearly differ in their strategies to cope with thermal stress in combination with high irradiance.