To elucidate what determines plankton community structures in subtropical and tropical oceans, cell size distributions of pico-and nanophytoplankton were extensively measured throughout the North and South Pacific Ocean. Mean cell sizes of three different populations, Synechococcus, nano-sized cyanobacteria, and eukaryotes, showed a clear diel cycle with a peak in the late afternoon. After subtracting the effect of the diel variation by fitting sine curves, the mean cell sizes of the three populations were regressed against temperature and nutrient concentrations. The multiple regression analyses revealed that a positive correlation between the cell size of eukaryotes and temperature was the only significant parameter. Size histograms demonstrated that in the warm waters, the contribution of pico-sized eukaryotes to total phytoplankton biomass was relatively small, which in combination with the numerical dominance of Prochlorococcus caused bipolarization of the size spectrum of the entire pico-and nanophyto-plankton community. These results demonstrate that commonly used biogeochemical models require amendment to account for the fact that an increase in sea surface temperature will simply lead to a prevalence of smaller phytoplankton. To reveal the effect of temperature on the entire food web, extensive surveys of zooplankton community structures will be required in future studies.