Abstract: Based on the multi-discipline investigation in 28th February-10th March and 30th May-4th June, 2005, this paper studied the distribution of sizefractionated phytoplankton in the Yangtze River estuary and its adjacent waters, and the environmental factors that affected this distribution. The results showed that in winter, the average chlorophyll a concentration was 1.28 mg·m^-3, and the region with high concentration chlorophyll a was located near the river mouth. Small-sized phytoplankton (SSP, <20 μm) contributed 66.7% to the total phytoplankton biomass, but big-sized phytoplankton (BSP, >20 μm) was dominant in the plume system. In spring, the average chlorophyll a concentration in inner river and outer estuary was 0.67 and 6.03 mg·m^-3, respectively, and the maximum of chlorophyll a concentration appeared in the waters between 122.5° E and 123.0° E. The SSP dominated in the plume system, especially in the algal bloom frequently occurring area which located at south of survey area, contributed 83.5% to the total phytoplankton biomass. The vertical profile of size-fractionated chlorophyll a showed that with the increase of water depth, the SSP and BSP became equal in the offshores. Among the environmental factors in the Yangtze River estuary and its adjacent waters, salinity and nutrients were the main factors affecting the distribution and composition of size-fractioned phytoplankton biomass in winter and spring.