Microbial communities were obtained from surface sediments of the Xisha Trough using cultured-independent technique. The characterization of the 16S rDNA gene amplified from the sediments indicated that archaeal clones could be grouped into the Euryarchaeota and Crenarchaeota domains respectively. Two archaeal assemblages, the Marine Crenarchaeotic GroupⅠ (49.2% of the total archaeal clones) and the Terrestrial Miscellaneous Euryarchaeotal Group (16.9%), were the most dominant archaeal 16S rDNA gene components in sediments. The remaining sequences were related to members of the Marine Benthic Group B (9.7%), Marine Benthic Group A (4%), Marine Benthic Group D (1.6%), Novel Euryarchaeotic Group (0.8%) and C3 (0.8%). The bacteria clones exhibited greater diversity than the archaeal clones, with the 16S rDNA gene sequences from members of the Proteobacteria (30.5% of the total bacterial clones), Planctomycetes (20.3%), Actinobacteria (14.4%), Firmicutes (15.3%), Chloroflexi (8.5%), Acidobacteria (34%), candidate division OP8 (2.5%), Bacterioidetes/Chlorobi (1.7%) and Verrucomicrobia (1.7%). Most of these lineages represented uncultured and undescribed groups of bacteria and archaea. The results suggest that a vast amount of microbial resource in the surface sediment of the South China Sea is yet to know.