Methanogens play a critical role in the process of soil carbon cycle in paddy soil, while the community and environmental factors of methanogens in salt-tolerant paddy fields are still unclear. Three soil samples were collected from Shangma rice improvement base in Chengyang district, Qingdao, including salt-tolerant paddy fields, ordinary paddy fields and control soils in different months. The abundance and structural characteristics of methanogens communities in different soil were revealed by real-time fluorescence quantitative PCR and Illumina high-throughput sequencing technology.