The effective transportation of picophytoplankton to the mesopelagic layer in the ocean by cell aggregation and attachment to large particles has been reported. Those findings suggest that picophytoplankton play important roles in ecological processes in the deep ocean. However, there is no information about vertical transportation of picophytoplankton cells from the epilimnion in lakes, though the presence of picophytoplankton cells in the hypolimnion has been reported. The present study demonstrated the possible importance of Synechococcus (Cyanobacteria) in ecological processes of the hypolimnion in the deep mesotrophic Lake Biwa, Japan. The chlorophyll a concentration in the 0.2-2.0-µm fraction, which is mainly derived from Synechococcus, accounted for a large portion (up to 28.8%) of the total chlorophyll a concentration in the hypolimnion during the thermal stratification period. We found a significant positive correlation between Synechococcus abundances in the epilimnion and hypolimnion during the stratification period. In addition, our incubation experiment revealed that Synechococcus did not show significant growth during the first 2 d in dark conditions. These results suggest the recent delivery of a significant fraction of Synechococcus cells from the epilimnion to the hypolimnion. Our results indicate that the abundance of Synechococcus makes a greater contribution to ecological processes in the hypolimnion of Lake Biwa than previously hypothesized, and this may also be the case for other deep lakes.