Combined methods of size fractionation and single-cell isolation were used to investigate the seasonal variation of phytoplankton dynamics in Tokyo Bay with an emphasis on primary productivity. Red tides occurred in Tokyo Bay from spring to autumn; a diatom, Skeletonema costatum, and a raphidophycean, Heterosigma akashiwo, were the most important primary producers. Small diatoms and flagellates, including these species, were dominant and showed rapid changes of phytoplankton community structure within several days in summer. The nanoplankton (3-20 mu m) fraction contributed most to chlorophyll a concentration and primary productivity during spring to autumn, whereas the microplankton (>20 mu m) contribution was remarkable in winter. Picoplankton (<3 mu m phytoplankton) remained relatively constant throughout the year. A significant reverse relationship was obtained between assimilation rate and chlorophyll a content for the total and nanoplankton population; the assimilation rate was high at the initial phase of the bloom, then decreased to a minimum level at the peak of the bloom. Factors controlling the reduction of assimilation rates at the peak, and changes in phytoplankton community structure, are discussed.