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In order to investigate the microbes in formation water samples from Well Du 6-3 and Ao-7 in the Alaxin and Aonan gas fields, Songliao Basin, China, 16S rDNA was amplified by using the Polymerase Chain Reaction (PCR) technique with templates of the extracted DNA and primers of bacteria and archaea. The PCR products were also inserted into vectors and then ligated with competent cells for gene sequencing. Based on the obtained gene sequences, bacterial and archaeal libraries were constructed and microbiological phylogeny graphs were obtained for the samples to understand the structure of microbial community and deduce the possible pathways of methanogenesis. The result indicates that there are only a few types of microbes in the samples of the two wells. Pseudomonas and Methanobacterium are the dominant species in the microbial and archaeal libraries, respectively. It is concluded that the indigenous microbial community in Well Du 6-3 probably mainly generated methane by CO2 reduction, but methanogenesis of acetic acid could not be completely excluded. The methane from Well Ao-7 is shown to have been definitely converted from CO2. Therefore, methane generation via indigenous microbial metabolism may be ultimately realized by using the right method under favourable conditions in the two fields. Key words: biogas reservoir, polymerase chain reaction (PCR), methane bio-pathway, 16S rRNA clone library