Abstract: The microscopic planktonic algae are the main primary producers in the marine ecosystem and play a very important role in marine food webs. They are critical food for filter feeding bivalve shellfish, such as oysters, mussels, scallops, clams, as well as the larvae of commercially important crustaceans and finfish. In normal cases, the proliferation of planktonic algae is beneficial for aquaculture and wild fisheries operations. However, in some cases, algal blooms caused by toxic or harmful algal species can have a negative effect, causing heavy losses to aquaculture, the fisheries industry and tourism operations, and having major environmental and human health impacts. For better understanding and assessment about the marine ecosystem in Nanji Islands National Nature Reserve, its phytoplankton community was characterized based on four cruise surveys carried out from May 2006 to February 2007, which may support many useful data and provide helpful guides for the ecological studies and protection of Nanji Islands National Nature Reserve. Species composition, seasonal variations and vertical distribution of microalgae as well as several chemical parameters were investigated. And the connections between microalgae dynamics and several environmental factors, such as water temperature, salinity, nitrogen and phosphorus nutrition concentration, were analyzed. A total of 80 species were identified, belonging to four phyla. These taxa could be classified into three ecotypes, in which the eurythermal species were dominant. Prorocentrum triestinum and Skeletonema costatum were the absolutely dominant species in spring and summer respectively and the dominant species in autumn and winter were various and polytype. Up to 71.25 percent of total taxa, 57 red tide causative species were observed, in which, diatom species were dominant and more harmful/toxic taxa were dinoflagellate. The blooms caused by P. triestinum and S. costatum occurred in spring and summer respectively. Decline trend of species number indicated from spring, summer, autumn to winter. Annual average cell abundance was 1.03×106cells/L. The cell abundance reached the peaks in spring and summer, both nearly up to 2×106cells/L, and their highest richness occurred in the near-shore waters where located at the north-west to Nanji Island. With low cell abundances about 103cells/L in autumn and winter, their richness centers shifted to the near-shore waters where situated at the south-east to Nanji Island. Shannon-Wiener index (H’) peaked in autumn (1.75) and minimized in winter (0.32). Using correlate analysis by SPSS, it is revealed that there is no obvious correlation between microalgae dynamics and any environmental factors. During the bloom of P. triestinum in spring, the ratio of nitrogen to phosphate nutrition maximized (34.01) because more phosphate nutrition has been absorbed by dinoflagellate cells than nitrogen nutrition. And the reverse situation occurred during the bloom of S. costatum in summer, the ratio minimized (7.81) because more nitrogen nutrition has been consumed by diatom cells. It was caused by the distinct nutrient habits of different bloom causative taxa in different seasons.