The Tropic of Cancer goes through the center of Taiwan separating it into two climate zones. Currents that pass through Taiwan also have an effect on the sea surface temperature (SST). The coral communities in Taiwan could be classified into two major clusters which congruent with SST and currents. This study was to investigate the relationship between SST and Symbiodinium communities in Galaxea fascicularis. Galaxea fascicularis is widely distributed in the reefs of Taiwan, which is a good model for spatial variation study. Symbiodinium communities were examined in G. fascicularis at two depths (3 m and 6 m) around the coasts of Taiwan main island and the surrounding islands. The mitochondrial cytochrome oxidase I (COI) gene and nuclear