Abstract: The phytoplankton species composition, quantity distribution, diversity, community structure and its relationship with the environmental factors inShacheng Harbour sea area in the northern Fujian Province were analyzed based on the survey in April, 2006. One hundred and fifteen species were identified, among which coastal eurythermic species were predominant, showing obvious characteristics of subtropical population fauna. The results showed that the average abundance of phytoplankton in Shacheng Harbour was 3113.24 indL-1. The abundance was higher in the inner bay than that in the outer bay in horizontal distribution. The surface abundance was a little higher, but there was no significant gradient in different water layers in vertical distribution. Shannon-Wiener diversity index, Margalef richness index, Pielou evenness index and Simpson dominance index were 2.390, 2.650, 0.726 and 0.306, respectively. Phytoplankton community structure was analyzed by PRIMER software. It showed that the community structure was divided into two groups of inner bay group and outer bay group, with the former being higher heterogeneity. The major environmental factors were DO, pH, NO3 and SiO4. The phytoplankton community structure and environmental factors was significantly correlated (P＝0.1%) with correlation coefficient of 0.372. The subset of environmenal variables (pH, NH4, SiO4) matched phytoplankton community structure best, with correlation coefficient of 0.701.