Abstract: Coral reefs are one of the typical environmentally sensitive marine ecosystems, and their response to environmental changes and adaptation mechanisms have received increasing attention. Understanding the genetics of the widely distributed species Pocillopora damicornis in the South China Sea is of great benefit to further understand the environmental adaptation mechanism of coral reefs in the South China Sea. Based on 84 P. damicornis samples collected from 2 typical sea areas and 4 survey stations in the South China Sea, this study characterized their genetic diversity and genetic structure based on 7 microsatellite markers. The statistical results of genetic diversity indicators showed that the level of genetic diversity of P. damicornis in the South China Sea was low（H_o is 0.090～0.567, H_e is 0.137～0.458）, and there was no significant difference in genetic diversity levels between the Hainan island and Xisha islands, among which the genetic diversity of Luluitou（Hainan island） was the higher, and that of Yinyu（Xisha islands） was the lowest. The results of genetic structure analysis showed that P. damicornis in the South China Sea formed two lineages of genetic separation:（Luluitou, Qilianyu, Yongxing） and Yinyu.The Mantel test results showed that there was no significant correlation between genetic differentiation among P. damicornis populations and average sea surface temperature（SST）（R~2=0.312 5, P=0.290）, SST variance（R~2=0.066 8, P=0.680）, geographic distance（R~2=0.048 4, P=0.680）, chlorophyll a concentration（R~2=0.107 2, P=0.480） and diffuse attenuation coefficient for downwelling irradiance at 490 nm（R~2=0.109 1, P=0.390）. These results showed that the lack of genetic diversity of P. damicornis populations are not conducive to the adaptation of this species to the severe ecological conditions, which means that the ability to recover after interference was poor and the risk of local extinction was high. This study evaluated preliminarily the genetic status and characteristics of the South China Sea（in two typical sea area） P. damicornis, which has modest reference value for the future protection of this species.