A survey was carried out from April 2006 to March 2007 in four sampling stations in Nanji Islands Sea Area, Zhejiang Province. Water samples, ambient chemical, physical and meteorological data were examined. Species composition, ecological distribution and seasonal dynamics of both diatoms and dinoflagellates were investigated. 93 taxon of phytoplankton were identified. Diatoms were the most diversified assemblage that 68 taxa belonging to 35 genera were found. And dinoflagellates ranked second with 21 taxa in 11 genera. The annual average phytoplankton cell abundance was 3.19105cellsL-1. The highest and higher cell abundance of diatom almost occurred in the summer and autumn. And diatom cell abundances in water surface levels were higher than that in bottom levels. One bloom of diatoms has been recorded, arising in August. And the dominant taxon was Skeletonema costatum. Dinoflagellate blooms just occurred in the spring and the dominant taxa were Prorocentrum species. The blooms of Prorocentrum triestinum and P. donghaiense occurred in middle May and later May respectively. More dinoflagellate cells distributed in the upper water surface levels than in bottom levels.