Anthropogenic discharges of nitrogen (N) and phosphorus (P) have caused widespread threats to coastal ecosystems. Bacterioplankton are known to play crucial roles in N/P cycling in marine environments, but little is known about how bacterioplankton community responds to N-P co-pollution. Here, we collected surface seawater samples along a transect in East China Sea. We applied 16S rRNA gene amplicon pyrosequencing to investigate the spatial variation of bacterioplankton communities under a N-P co-pollution gradient. The bacterioplankton communities were dominated by Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes and Betaproteobacteria, which were distinct from those of sediment bacterial assemblages at the same transect. The bacterioplankton community compositions (BCCs) did not vary consistently along the pollution gradient, but clustered into nearshore and offshore groups. The combined environmental factors and spatial distances contributed 30.4% and 12.2% to the variation of the BCC, respectivelys, with a high auto-correlated effect that constrained 25.8% variation. In addition, a series of sensitive bacterial OTUs were identified, whose abundances were significantly associated with the N and/or P levels. This study demonstrates that coastal N-P co-pollution dramatically alter the BCCs, while these changes could be characterized by a few sensitive bacterioplanktonic OTUs.