Abstract: Surface waters were collected monthly from Lingshui bay and Xincun bay of Hainan province for analysis of phytoplankton pigments by using HPLC from December 2010 to May 2011. The temporal and spatial distributions of phytoplankton community were calculated using CHEMTAX. Furthermore, the relationships between the phytoplankton community and environmental factors were discussed. The results showed that the concentration of most pigments decreased from Xincun bay to Lingshui bay. Fucoxanthin and chlorophyll a were the two major pigments in Lingshui bay and Xincun bay, with an average of 0.53 μg/L and 0.22 μg/L, respectively. CHEMTAX conformed that the dominant algal groups were diatoms. However, the picophytoplankton and nanophytoplankton in Lingshui bay, such as Prasinophytes, Cyanobacteria and Chrysophytes, were higher than Xincun bay, indicating the miniaturizing tendency of phytoplankton community toward Lingshui bay. Statistical analysis revealed that the distribution of phytoplankton were obviously controlled by environmental factors, including temperature and nutrients.