Vertical variations of bacterial community composition in the South China Sea was investigated on 18 September 2009 by denaturing gradient gel electrophoresis (DGGE) and analyzed by multivariate analysis. Twenty-seven sequences retrieved from DGGE bands fell into five groups based on BLAST analysis. The dominant bacteria were Cyanobacteria (35.7%) and Proteobacteria (39.2%). The DGGE profile showed Proteobacteria mostly obtained from samples from the deeper layers while sequences related to Cyanobacteria only existed in the euphotic layer. Other phylogenetic groups have been identified as Firmicutes (10.7%), Actinobacteria (7.1%), and Deinococcus-Thermus (3.6%). The unweighted pair group method with arithmetic mean has been employed to cluster the samples, and results indicated that all samples tended to group together on the basis of depth and could be further subclassified into two subgroups: Group I (including samples from 0 m, 50 m, 75 m, 100 m, and 150 m) and Group II (including samples from 200 m, 400 m, 500 m, 600 m, 700 m, and 900 m). Canonical correspondence analysis revealed the temperature was the most significant factor in determining the vertical distribution of the bacterial community (P=0.018, P<0.05).