Seasonal abundances of phototrophic picoplankton (PP) and heterotrophic nanoflagellates in Lake Biwa were studied from 1994 to 1998. Seasonal variation in cell volume and biomass of the phototrophic picoplankton were also studied. PP were counted using disposable glass microscopic plates, which gave superior accuracy to sample filtration onto membrane filters. Phycoerythrin-rich rod-shaped cyanobacteria (PEC), one of the major components of the picoplankton community, were sparse (about 10 4 cells ml )1 ) in winter and began to increase in April. Several PEC peaks were observed during the period of thermal stratification, and a rapid fall took place after October or November. In the northern basin, PEC peaked during late June and early July in 3 of the 5 years, and in late summer in the remaining years. Phycocyaninrich rod-shaped cyanobacteria (PCC) were abundant in the southern basin and were present in smaller numbers in the eutrophic nearshore area of the northern basin; they peaked several times during the period from July to October. Seasonal variations of these two kinds of picoplankton were correlated with seasonal changes in water temperature. Phycoerythrin-rich cylinder-shaped cyanobacteria exhibited narrow peaks in July, their abundance declining as the year progressed. The density of heterotrophic nanoflagellates was greatest in early spring. Average cell volume of PEC was largest in winter, then decreased gradually to a minimum in late summer; after the fall, it recovered to the winter cell volume. This change can likely be attributed to the depletion of nitrogen in the warmer seasons.