There has been an increasing recognition in recent years that many phytoplankton species are not simply photoautotrophs, but actually possess highly flexible feeding strategies, collectively referred to as mixotrophs.  Mixotrophic nanoflagellates are responsible for up to 40–95% of the total bacterivory in a variety of environments and make major contributions to phagotrophy in the microbial food web.  The South China Sea is one of the largest marginal seas in the world, an important part of the earth's climate system.  This study aimed to investigate the phagotrophy in mixotrophic nanophytoplankton in the surface layer and DCM layer of the euphotic zone in the northern South China Sea.  We estimated the rates of bacterial ingestion by Chlorophyta, Prymnesiophyceae, Pelagophyceae and Mamiellophyceae using fluorescently labeled bacteria (FLB) and fluorescence in situ hybridization with tyramide signal amplification (TSA-FISH).  Their abundances were also investigated in the same sampling area.  The specific grazing rates of Chlorophyta, Pelagophyceae and Mamiellophyceae decreased with the increase of nutrient concentration, indicating that these groups preferred the phagotrophy in the surface layer.  According to the grazing effect, Prymnesiophyceae, Mamiellophyceae and Pelagophyceae are key phago-mixotrophic nanophytoplankton in the euphotic zones of northern South China Sea.