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, ¹⁶Sr DNA was amplified using the Polymerase Chain Reaction (PCR) technique with templates from 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. Methane generation via indigenous microbial metabolism may be ultimately realized using the right method under favorable conditions in the two fields. It is concluded that the indigenous microbial community in Well Du 6-3 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.