The bulk DNA was isolated from bacterial habits in sediments of the Xisha trough, the south China sea. Using a pair of primers special for most common bacteria, the researchers amplified partial sequences of bacterial 16S rDNA gene and thus constructed a 16S rDNA clone library. A total of 22 clones were used to reconstruct the bacterial 16S rDNA phylogenetic tree. Guided by the phylogenetic tree, bacteria fell into four main lineages: Proteobacteria, Planctomycene, Actinabacteria and Low G+C Gram-positive bacterium. Among them, 49% belonged to Proteobacteria, 22% to Planctomycene,the same to Low G+C Gram-positive bacterium,and the remaining 7% to Planctomycene. The group of Proteobacteria clustered in three subgroups: α-, γ- and δ-Proteobacteria, and the subgroup of δ-Proteobacteria predominated in them. Furthermore, the abundance of two groups of Planctomycene and Low G+C Gram-positive bacterium, living commonly in shallow marine deposits, was higher in sediments of the Xisha Trough than in other deep-sea sediments. Most members of these two groups were probably brought from the shelf into the trough sediment by the turbid.