Methanogens and sulfate reducing bacteria were detected by the 16SrRNA sequencing of coalbed methane (CBM) co-produced water in the south of the Qinshui Basin, which is indicative of the presence of secondary biological gas in the south of this basin, in contradiction to the previous understanding of thermogenic gas. This work systematically collected water samples from the CBM wells in the Shizhuangnan Block and analyzed the microbial geochemical characteristics from the aspects of water ions, hydrogen and oxygen isotopes, dissolved inorganic carbon and microbial diversity. It is shown that the Shizhuangnan Block has a nearly SN-trending monoclinic structure, and the elevation of coal seam decreases gradually from the east to west. Because of the water blocking effect of Sitou fault in the west, the precipitation flowed from the east to west, and gradually transited to stagnant flow area. The concentration variation of some ions such as Na+, K+, Ca2+, Mg2+, Cl?, HCO3? and total dissolved solids (TDS) suggest the variation of redox condition in the coal reservoir water. The 16SrDNA sequencing analysis of the collected water samples detected the presence of methanogens and sulfate reduction bacteria. The presence of methane production zone and sulfate methane transition zone (SMTZ) was identified. The effect of methanogens in the methane production zone leads to an increase in the methane concentration, resulting in a high gas content in the study area. In the SMTZ, most methane is consumed by anaerobic oxidation due to high sulfate concentrations.