Abstract: Sampling was carried out in April 2010 and August 2011 in order to study the structure of phytoplankton community and its relationship with environment factors by software CHEMTAX in different seasons in the Bamen bay. The main results are as follows:the biomass increased from the Wenchang River to sea and appeared the maximum value in the river mouth to the Bamen bay. Chrysophytes and Chlorophytes were dominant groups in spring 2010. The biomass was positively correlation with dissolved inorganic nitrogen (DIN), SiO₃^2- and PO₄^3- in spring, while negatively correlation with salinity. There was little correlation between phytoplankton and nutrients ratios (N:P ratio, Si:N ratio). But Diatoms was positively correlation with PO₄^3-. The biomass didn't show any apparent trend in summer 2011. And the maximum of biomass was in the bay. As to phytoplankton, Cyanobacteria, Chrysophytes and Diatoms were important groups in summer 2011. The biomass was positively correlation with SiO₃^2-, while negatively correlation with salinity. There was obvious correlation between phytoplankton and nutrients ratios. The abundance of chlorophytes was positively correlation with N:P ratio and N, while the abundance of diatom was positively correlation with Si:N ratio.