The diversity of symbiotic algae of the genus Symbiodinium (Symbiodinium sp.) within a widespread ranging scleractinian coral Galaxea fascicularis along latitudinal gradients in the South China Sea was examined using restriction fragment length polymorphism (RFLP) of the large subunit rDNA and sequencing. It revealed that G. fascicularis was associated with two distinct zooxanthellae clades. Galaxea fascicularis sampled in Daya bay in Guangdong province harboured Symbiodinium Clade C, while G. fascicularis sampled in Sanya Bay of Hainan Island, Yongxing Island of Xisha Islands, and Zhubi Reef of Nansha Islans harboured Symbiodinium Clade C and D either simultaneously or sequentially, indicating symbiosis flexibility. A distinct latitudinal distribution of Symbiodinium sp. in G. fascicularis was also revealed. Galaxea fascicularis hosting two clades of Symbiodinium sp., especially Symbiodinium clade D, may provide hosts with a flexible mechanism for adaptation to environmental change and can more easily survive mass coral bleaching events.