[Objective] To analyse methanogenic community and the pathway of biogenic methane in the formation water from coalbed methane (CBM) wells in the Qinshui Basin. [Methods] Based on the methyl coenzyme-M reductase (mcrA) gene, the diversity of methanogens from different CBM wells formation water were investigated by 454 pyrosequencing and aligning mcrA sequences from NCBI functional genes library. [Results] The high-throughput sequencing indicated that the numbers of OTUs (Operational taxonomic units) were 64 to 157 in five detected methanogens communities, only 22 OTUs were identical in all samples, which accounted for 14% to 34% in each sample. According to the alignment results of high-throughput sequencing data and mcrA library, four genera were detected in five formation water, including Methanobacterium, Methanomicrobium, Methanolobus and Methanospirillum, the dominant genus was Methanobacterium. Phylogenetic analysis indicated that the majority of unidentified genera were closely related to Methanobacterium, Methanomicrobium, Methanococcus and Methanoculleus. Although the percentage of methanogens was different in five sample, the detected genera were about the same. The hydrogenotrophic methanogenesis was main pathway of methane formation in the Qinshui Basin. [Conclusion] The methanogens species were obvious different in different CBM blocks of the Qinshui Basin. However, methanogenesis pathways were similar and had no correlation with the geographical location and reservoir conditions.