The South China Sea is one of the largest marginal seas in the world. A cruise was conducted during September 2005 to investigate the spatial distribution of viral and bacterial abundance as well as nutrient and chlorophyll a (chl a) concentrations in the northern South China Sea (SCS). The northern SCS was divided into 3 regions: the estuarine coastal plume, continental shelf, and open ocean. Except for the estuarine coastal waters, the northern SCS is oligotrophic. The distribution of chl a and viral and bacterial abundances were closely related to the water mass since higher chl a and viral and bacterial abundances occurred in the upwelling region and the cold eddy. Viral and bacterial abundances decreased from the estuarine waters to offshore waters. On average, viral abundance was significantly higher (p < 0.05) in the estuarine coastal plume (25.2 ᠳ.1 נ106 ml -1), than on the continental shelf (14.1 ᠶ.5 נ10 6 ml-1) or the open ocean (11.7 ᠵ.3 נ106 ml-1). Bacterial abundance followed a similar spatial distribution, ranging from 4.6 ᠱ.1 נ106 ml -1 in the estuary to 1.6 ᠰ.8 נ106 ml-1 in the open ocean. Ratios of viral to bacterial abundance (VBR) increased from near-shore to the coast and open ocean (5.6 ᠰ.7, 6.1 ᠲ.2 and 8.4 ᠴ.7, respectively). This is due to the fact that viral abundance decreased slower than bacterial abundance from the estuarine plume to the open ocean. Viral abundance was more significantly correlated with bacterial abundance (p < 0.0001) than with chl a concentration (p = 0.001), suggesting that bacteria were the major host members for marine viruses in the oligotrophic northern SCS. The highest abundance of viruses highlighted the significant influence of the relatively nutrient- and organic-rich Pearl River outflow on the northern SCS and indicated that viruses also responded to anthropogenic inputs in marine ecosystems.