Microbial community structures in the Arctic deep-sea sedimentary ecosystem are determined by organic matter input, energy availability, and other environmental factors. However, global warming and earlier ice-cover melting are affecting the microbial diversity. To characterize the Arctic deep-sea sediment microbial diversity and its relationship with environmental factors, we applied Roche 454 sequencing of 16 S r DNA amplicons from Arctic deep-sea sediment sample. Both bacterial and archaeal communities’ richness, compositions and structures as well as taxonomic and phylogenetic affiliations of identified clades were characterized. Phylotypes relating to sulfur reduction and chemoorganotrophic lifestyle are major groups in the bacterial groups; while the archaeal community is dominated by phylotypes most closely related to the ammonia-oxidizing Thaumarchaeota(96.66%) and methanogenic Euryarchaeota(3.21%). This study describes the microbial diversity in the Arctic deep marine sediment(>3 500 m) near the North Pole and would lay foundation for future functional analysis on microbial metabolic processes and pathways predictions in similar environments. Microbial community structures in the Arctic deep-sea sedimentary ecosystems are determined by organic matter input, energy availability, and other environmental factors. However, global warming and earlier ice-cover melting are affecting the microbial diversity. To characterize the Arctic deep-sea sediment microbial diversity and its relationship with environmental factors, we applied Roche 454 sequencing of 16 S r DNA amplicons from Arctic deep-sea sediment sample. Both bacterial and archaeal communities’ richness, compositions and structures as well as taxonomic and phylogenetic affiliations of identified clades were characterized. Phylotypes relating to sulfur reduction and chemoorganotrophic lifestyle are major groups in the bacterial groups; while the archaeal community is dominated by phylotypes most closely related to the ammonia-enriched Thaumarchaeota (96.66%) and methanogenic Euryarchaeota (3.21%). the microbial diversity in the Arctic deep marine sediment (> 3 500 m) near the North Pole and would lay foundation for future functional analysis on microbial metabolic processes and pathways predictions in similar environments.