Protists grazing and viral lysis are the main causes of bacterial mortality, and both processes influence structures of bacterial communities in marine systems. Here, using dilution experiments, we altered the strength of protist grazing pressure and viral lysis effect and investigated how bacterial composition is shaped by these processes in the southern East China Sea. Microbial abundances and compositions were obtained through flow cytometry counting and sequences of 16S rDNA with illumina Miseq, respectively. Specifically, we investigated the relationships between the taxon-specific net growth rate versus the strength of protist grazing and viral lysis for five main bacterial classes Our results showed contrast results among taxa. While Proteobacteria (the most dominant class occupying 85% relative abundance on average) net growth rates decreased with increasing grazing and viral pressure, the net growth rate of Actinobacteria, Planctomycetes, SAR406, and Bacteroitetes showed the opposite pattern. Our results indicate that predators suppress the most dominant taxon, which stimulates growth of the other taxa, supporting “Kill the winner hypothesis”. Our findings indicated a taxon-selective effect from protists grazing and viral lysis that shape bacterial communities in a natural marine ecosystem.