Abstract: In this study, Illumina high-throughput sequencing technology and real-time quantitative PCR (RT-qPCR) were used to profile the archaeal community and vertical distribution in the surface, middle and bottom sediments of Pearl River Mouth Basin in the northeastern South China Sea. The results showed that the majority of archaeal sequences were classified into Thaumarchaeota, Woesearchaeota, Bathyarchaeota and Euryarchaeota. The archaeal community diversity and richness in the surface sediment were lowest in three samples, in which Marine Group I (MGI) was most abundant; in contrast, the main groups were MGI, Group C3, Marine Benthic Group B and Thermoplasmata in the middle and bottom sediments. Interestingly, Nitrosopumilus related to ammonia oxidation was dominant in the sediments, suggesting that nitrogen metabolism was probably active. RT-qPCR results illuminated the abundance of archaea ranging from 2.00×10⁷ copies/g to 8.20×10⁷ copies/g decreasing with the increasing depths. These results will provide a basis for further study of the archaeal community characteristics in the sediments of South China Sea.