【Summary】The sediment samples were collected from Maluku Strait at a depth of 1250 m, which is influenced by Mindanao Current and Indonesian Throughflow. Based on 16S rRNA clone libraries, the community structure and vertical distribution of archaea and bacteria were studied in a columnar sediment of 2m in length. From the surface sediment, 16S sequences were derived from fourteen bacterial phyla (Gammaproteobacteria, Planctomycetes, Alphaproteobacteria, Deltproteobacteria were dominant), but were limited to two groups of archaea: Crenarchaeota (99%) and Euryarchaeota (1%). Besides, 90% of the archaea clones were ammonia oxidation-related which indicated that the ammonia-oxidizing archaea might make a significant contribution to the chemosynthesis in the surface sediment. Contrastively in the bottom sediment, six bacterial phylogenetic groups were obtained (Gammaproteobacteria and Firmicutes were absolutely dominant), however no archaea 16S rRNA was detected. The microbial diversity of surface sediment was much higher than the bottom and seven unique bacterial phyla were obtained from two sediment respectively. The geochemical elements analysis revealed that the content of C, TOC and S in the surface sediment was much higher than the bottom, but the content of P is contrary. The microbial communities might be in response to the geochemical substance transfer and deposit influenced by the ocean current and it deserves further study compared with the other sediment samples in this area.