Preliminary characterization of the microbial phylogeny and metabolic potential of a deep-sea sediment sample from the Qiongdongnan Basin, South China Sea, was carried out using a metagenomic library approach. An effective and rapid method of DNA isolation, purification, and library construction was used resulting in approximately 200,000 clones with an average insert size of about 36 kb. End sequencing of 600 individual clones from the fosmid library generated 1,051 sequences with an average sequence length of 619 bp. Phylogenetic ascription indicated that this library was dominated by Bacteria, predominantly Proteobacteria, though Planctomycetes were also relatively abundant. Sulfate-reducing and anaerobic ammonium-oxidizing bacteria, which play important roles in the cycling of sedimentary nutrients, were abundant in the library. Cluster of orthologous groups category analysis showed that most of the genes contained in the end sequences were related to metabolism, and with cellular processes and signaling. Functional groups assigned by SEED (subsystems-based annotations) highlighted the existence of 'one-carbon' metabolism within this community as well as identifying functional genes involved in methanogenesis. Furthermore, diverse genes involved in the biodegradation of xenobiotics were found using Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis.