It is generally believed that biogenic coal bed methane (CBM) is an end product of coal biodegradation by methanogenic archaea and syntrophic bacteria. In this work, the archaeal and bacterial communities of CBM reservoir associated with Ordos Basin in China were investigated using 454 pyrosequencing. Sampling produced water, coal and rock in the reservoir, a total of 46,598 sequence reads were obtained. All archaea were methanogens with the genus Methanolobus predominating. The genus consisted of 81.18% of pyrosequencing reads in water sample and >99% in coal and rock samples. Although the phylum Proteobacteria was the main component of all samples, bacterial communities in coal and rock samples were similar at the genus level, which were distinctly separated with water sample. The results strongly suggested that methylotrophic methanogenesis governed the biogenic CBM formation. The separation of microbial communities between water and coal, rock samples should be considered when investigating the process of coal biodegradation and the generation of new biogenic CBM. (C) 2012 Elsevier B.V. All rights reserved.