[Objective] The archaea are recognized as key players participating in the global biogeochemical cycles in marine sediments. The knowledge upon community structure and metabolic functions of archaea is the basis to understand their potential contributions on the biogeochemical cycles globally. [Methods] Archaeal diversity in the sediments of three areas at the northern continental slope of SCS was surveyed using high-through sequencing for 16S rRNA gene. [Results] The major archaeal groups in the sediments was found to include Bathyarchaeota, Thermoplasmata, Woesearchaeota (DHVEG-6), Thaumarchaeota (Marine Group I), Lokiarchaeota and Marine Hydrothermal Vent Group (MHVG), also with low abundant of AK8, Marine Benthic Group A and Terrestrial Hot Spring Crenarchaeota Group (THSCG). Anaerobic methane oxidation (AOM) microbes (Anaerobic methanotrophic archaea, ANME), mainly ANME-1, ANME-2ab and ANME-2c were also found in the potential gas hydrate zone. Methyl coenzyme-M reductase alpha subunit (mcrA) gene, which encodes the key enzyme in methane metabolism, was also recovered from these sites, implying potentially active methane cycling. Quantitative PCR results showed that the abundance for bacterial 16S rRNA gene, archaeal 16S rRNA gene and mcrA gene were 105?107 copies/g (wet weight), 105?106 copies/g (wet weight) and 103?105 copies/g (wet weight), respectively. [Conclusion] These results revealed high diversity of archaea and rich microbial recourses in SCS sediments, layed the foundation for further analysis and understanding of archaeal mediated carbon cycling in the sediments of SCS.