Abstract: Flow cytometry was used to follow the diel variations in abundance of Synechococcus spp. and picoeukaryotes in subtropical western Pacific coastal waters in June 2017. A modified dilution method was also used to estimate diel changes in the effect of nanoflagellate and viruses on Synechococcus spp. and picoeukaryotes. Obvious diel patterns were found in changes in abundance in both Synechococcus spp. and picoeukaryotes, the highest values recorded at night. Synechococcus spp. and picoeukaryotic growth decreased significantly in more highly diluted samples incubated during the daytime, suggesting that picophytoplankton production is partially dependent on grazing- and virus-mediated nutrient cycling during the daytime. At nighttime, nanoflagellate grazing and viral lysis were responsible for Synechococcus spp. mortality at rates of 0.02 h−1 and 0.04 h−1, respectively, and nanoflagellate grazing was responsible for all picoeukaryotic mortality. The most important finding of this study was that nanoflagellate grazing exerts great control over picoeukaryotes at night in these subtropical western Pacific coastal waters.