Coal bed methane generated thermogenically or biogenically is a significant unconventional natural gas resource. However, assessments of biogenic methane in high-rank coal deposits have been rarely reported. On the basis of geochemical and microbiological investigations of coal reservoir water, this is the first study of the Shizhuangnan block in southern Qinshui Basin, China that provides an understanding of methanogenic pathways and indigenous microbes. Carbon and hydrogen isotopes indicated that CO2 reduction and acetate fermentation methanogenesis coexisted in the Shizhuangnan block. The 16S rRNA results revealed that native archaea were dominated by Methanobacterium and Methanosarcina that were significantly affected by geochemical factors in the indigenous environment. As microbial consortia, the presence of various fermentative bacteria played a crucial role in coal biodegradation. In particular, sulfate-reducing bacteria competed with methanogens for substrates under relatively high sulfate concentrations. Finally, 16S rRNA sequencing indicated that acetate fermentation methanogenesis was more prevalent than CO2 reduction methanogenesis near the eastern outcrop in the study area.