We simultaneously examined seasonal fluctuations in maximum quantum yield (F-v/F-m), cell density and genotypic clade composition of zooxanthellae in the sympatric corals Pavona divaricata and P. decussata at a high latitude site in Okinawa, Japan. The 2 species had different responses to seasonal changes in light and seawater temperature. P. decussata was associated only with clade C zooxanthellae (at all sampling times) while genotypic clade composition fluctuated in P. divaricata. Three colonies of P. divaricata harbored clade D throughout the year and the other 7 colonies changed clade type from C to D or vice versa, or contained a mixture of both clades on some sampling occasions. Though neither coral species suffered bleaching during the experimental period, there were Fv/Fm decreases in P. decussata and P. divaricata harboring clade C during cold and warm seasons; F-v/F-m,, of P. divaricata harboring clade D was stable. When exposed to low or high temperature under normal or high light, P. divaricata harboring clade D was less damaged and Photosystem II recovery was faster than in P. decussata harboring clade C. These results suggest that the sympatric congeneric corals have different symbiont switching flexibilities and this difference might account for the observed difference in stress susceptibility between the two species. In high-latitude reefs, both winter low temperatures and summer high temperatures may be potential stressors that cause coral bleaching, at least in corals with high clade C zooxanthellar fidelity.