We monitored the abundance and biomass of nanoflagellates and their potential prey, heterotrophic bacteria, and Synechococcus spp. five times during the summers in 2010 and 2011. We used size-fractionation to measure growth and grazing rates of heterotrophic bacteria and Synechococcus spp. Temporal changes in surface water chlorophyll a (Chl a) concentrations during our study were caused by an influx of nutrient-rich water upwelling into the surface water. The bacterial growth rates ranged from 0.01 to 0.08 h-1 and grazing rates from 0 to 0.06 h-1. Bacterial growth rate had a positive relationship with Chl a concentration. Furthermore, growth and grazing rates of Synechococcus spp. ranged from 0.01 to 0.09 and 0 to 0.02 h-1, respectively. During the study period about 68% of the bacterial production and 41% of the Synechococcus spp. production was grazed by nanoflagellates in the southern East China Sea upwelling region, thus, a large fraction of bacterial biomass is transferred to higher trophic levels via nanoflagellate grazing.