Abstract: A cruise was conducted during November 2014, and water samples in 20 stations in the middle-north of the South China Sea were collected at 5 m, 25 m, 75 m, 150 m and 200 m layers, respectively. The distribution of virioplankton and bacterioplankton abundances in horizontal and vertical direction were studied by flow cytometry, and their relationships with environmental factors were also analyzed. The results show that the bacterioplankton and virioplankton densities in the water column were (1.19~151.65)×10⁴cells·mL^-1and (1.37~326.70)×10⁵ cells·mL^-1, respectively. Bacterioplankton abundance at 5 m and 25 m layers were (54.03±30.87)×10⁴ cells·mL^-1 and (4.94±4.15)× 10⁴cells·mL^-1; the number of virioplankton were (121.95±89.73)× 10⁵ cells·mL^-1 and (9.98±6.54)×10⁵ cells·mL^-1, respectively. According to the increase of water depth, the number of bacterioplankton and virioplankton both decreased gradually. Horizontal distribution of bacterioplankton and virioplankton show a similar variation tendency. Bacterial and viral abundances in most of the northern area stations were higher than those in the south at 5 m and 25 m layers. Impact factors of bacterioplankton and virioplankton varied at different water layers. Bacterioplankton and virioplankton distributions were positively correlated with phosphate (P < 0.05), a limiting nutrient factor in the surface water of the South China Sea. Bacterial distribution was significantly correlated with nitrate, silicate and total organic nitrogen at 75 m, where positive correlations between virioplanktion abundance and nitrate, silicate, total organic nitrogen and silicate were also detected. Correlation between environmental factors and bacterial and viral distributions may demonstrate the existence of top-down control mechanism. Virioplankton was positively related to bacterioplankton, which reflects a closely coupling between viruses and host cell abundance (P < 0.01).