Abstract: A detailed field survey of hydrological, chemical and biological resources was conducted in the southern waters of Miaodao Archipelago in autumn 2012.The distribution of phytoplankton and its response to environmental factors were investigated with multivariate statistical analysis techniques.Totally 94 taxa were identified.The abundance of phytoplankton was 6.65106 cells/m3 and gradually increasing from Miaodao Strait (close to land) to ocean (far away from land).Characteristics of phytoplankton assemblages were identified using principal component analysis (PCA), while redundancy analysis (RDA) was used to examine the environmental variables that may explain the patterns of variation of the phytoplankton community.Based on PCA results, the phytoplankton was mainly distributed in the eastern, western and northern water zone (waters far away from land).RDA indicated that depth, water temperature and total phosphorus had the most profound impacts on the phytoplankton assemblages.