To understand the genetic diversity and population changes in cyanophages in the coastal waters of Shantou, northeast South China Sea, we used the capsid assembly protein gene g20 as a marker of the abundance and phylogeny of natural cyanomyovirus communities. The abundance of total viruses, heterotrophic bacteria, and picophytoplankton in the coastal waters was monitored with flow cytometry. Hydrological parameters （NO3^-, NO2^-, NH3, soluble reactive phosphorus, total dissolved nitrogen, total dissolved phosphorus, dissolved oxygen, chemical oxygen demand, temperature, salinity, and chlorophyll a concentration） and microbial abundance （total viruses, total bacteria, Prochlorococcus, Synechococcus, and eukaryotes） were measured in the upper and lower layers at four sampling sites in the research area. In the direct viral counts, cyanomyoviruses accounted for 1.92% to 〉10% of the total viral community. A phylogenetic analysis showed that the g20 sequences in the Shantou coastal waters were very diverse, distributed in eight distinct operational taxonomic units, including the newly formed Cluster W. The g20 gene copies inferred from real time PCR assay indicated that cyanomyovimses were correlated significantly with the heterotrophic bacteria numbers and the nitrate and chlorophyll a concentrations. These results suggest that cyanomyoviruses are ubiquitous and are an abundant component of the virioplankton in Shantou coastal waters.
