Abstract: This study analyzed the nucleotide sequences of Internal Transcribed Spacer (ITS) from Symbiodinium of 20 coral species. A total of 47 samples were collected from Yangmeikeng sea area in Shenzhen. Through ITS sequence analysis, a Neighbor-Joining tree was constructed with 4 different Symbiodinium groups in GenBank. The results show that Symbiodinium of scleractinia corals in this sea area belong to 2 different species (subgroups), 19 samples belong to the C1 subgroup, 1 sample belongs to the C15 subgroup. The Symbiodinium’s genetic distance between C1 and C2 subpopulations is 0.01. Comparing with the Symbiodinium’s ITS sequences of C1 subgroup obtained from Yangmeikeng sea area in Shenzhen, the Dongshan sea area of Fujian Province and the Xuwen sea area of Guangdong Province, we found that the average (A+T) base content of algal samples is 49.4%, which is less than (G+C) in Yangmeikeng sea area. The construction of Neighbor-Joining tree shows that Symbiodinium from Dongshan and Yangmeikeng sea areas has a closer relationship compared with that from Xuwen. Thus, it is suggested that geographical isolation may be the main factor for the difference.