Significant coral bleaching was observed in summer in Shiraho reef, a fringing reef in the east coast of Ishigaki Island, Okinawa, Japan. To find relationship between coral bleaching and thermal stress in the reef and its governing factors, we have examined data obtained by field surveys in July 2003 and 2007 at Shiraho reef and the corresponding numerical simulation results for spatio-temporal variations of water temperature. The results of analysis showed that the spatial distribution of the degree of coral bleaching in the reef is closely related with that of the mean water temperature, which is strongly governed not only by local topography but also by meteorological conditions, especially latent heat flux.