Annual variation of phytoplankton community in coastal waters at western Hainan Island and its related affecting factors were analyzed based on four cruise surveys of four seasons carried out in 2008 and 2009. A total of 155 species (including 5 forms and 2 varieties) belonging to 74 genera of 4 classes were identified in 165 samples, in which diatoms were predominant in the species composition and the cell abundance. Dinoflagellates contributed the second major group. Cyanobacteria abundance increased in July. The dominant species were Thalassionema nitzschioides, Bacillaria paradoxa, Paralia sulcata, Chaetoceros curvisetus, Rhizosolenia styliformis, Trichodesmium spp., Prorocentrum micans, etc. Among them, Thalassionema nitzschioides, Bacillaria paradoxa and Paralia sulcata were dominant in four seasons. The species composition showed a significant seasonal change while phytoplankton cell abundance did not. Phytoplankton species were lower in October than in January, while richer in April and July. The annual average cell abundance of phytoplankton was (6.364.75)103 cells/L (n=165), and the peak cell abundance appeared in October. The phytoplankton abundance of each season reduced from near-shore waters to offshore. Patch distribution of Trichodesmium spp. were obvious in April and July. The diversity index was almost coincident with that of the Pielou evenness index. The high values of both index suggested that the phytoplankton community was in stability and the water quality was healthy in western Hainan Island. Pearson Correlate Analysis of phytoplankton cell abundance with environmental factors indicated that the phytoplankton abundance non-correlated to water temperature, correlated positively to the abio-notrogen in October, and negatively correlated to the salinity in January and to the abio-phosphate in July. The feeding stress from zooplankton directly affected annual variation of the cell abundance of phytoplankton along with influences of biological relationship even of ecosystem components.