Biogenic coalbed methane is produced by biological processes mediated by the synergistic interaction of microbial complexes in coal seams. However, the comprehensive ecological role of methanogenic archaea in biogenic coalbed methane production remains poorly understood. Here, we study the metagenome assembled genomes (MAGs) of Methanoculleus from coal seams, which were stimulated by minimal salts plus yeast media in anaerobic conditions. The Methanoculleus genus accounted for the highest proportion of archaea (80.4 ± 2.8%) once the CH4 concentration in the headspace increased to 15.0 ± 2.6% on the 50th day. The Methanoculleus MAGs were closely related to M. thermophiles; even so, 30 genes were detected in MAGs which were lacking in the genomes of M. thermophiles ATCC 33837. A deeper look at the metabolic pathway showed several metabolic pathways, including methanogenesis, glycolysis, urea cycle, TCA cycle and sulphur reduction. The CO2 and acetate were the primary carbon sources of these cells for the methanogenesis pathway. Glycolysis and sulphate reduction processes were the main processes for providing acetate. In addition, the cells had a variety of other functions, including nitrogen fixation and hydrogen production. Overall, this study enabled a better understanding of the ecological roles of Methanoculleus for biogenic methane in coal seams by combining bioinformatic techniques.