Using multivariate statistical techniques, the biogeography of phytoplankton community and its underlying environmental factors were studied in the coastal waters of northern Zhejiang. The results showed that 94species belonged to 40genera, 5phyla were recorded (with 9species were unclassified to genus level), of which predominated by diatoms, followed by dinoflagellates. Hierarchical clustering analysis (HCA) and analysis of similarity (ANOSIM) demomstrated that the study area could be divided into 3subareas accrding to the significant differences in phytoplankton community. Indicator species analysis (ISA) further confirmed that the indicator species of each subarea correlated significantly with specific environmental factors. Mantel test revealed that both the geographic distance and environmental heterogeneity (the levels of Silicate (SiO_3~(2-)), phosphate (PO_4~(3-)) and dissolved oxygen (DO), and pH value), contributed the variations in phytoplankton community. This pattern were further evidenced by partial Mantel test when the effect of environmental dissimilarity was held constant. Variation portioning analysis (VPA) revealed that the interactive effects of environmental and spatial factors were higher than the pure environmental variable or the pure spatial distance alone, suggesting that the biogeography of phytoplankton were mainly affected by both the environmental variability and dispersal limitation. Additionally, the unexplained variation may be attributed to other unmeasured factors (e.g., trace metals, biological grazing, climate change, and time-scale variation), which need further study.