With the development of molecular biology, the research on microflora in the environment is accelerated and a new research method for oil reservoir microflora is provided. Based on the methods of PCR-DGGE, the change of the structure of dominant microbial population in selectiveactivation of stratal bacteria was studied. During activation, the change of samples' DGGE bandings under different pressure conditions (1 MPa and 10 MPa) was analyzed, the PCR alignment analysis of bacteria was studied, the dominant bacteria at different periods were explored, the phylogenetic tree of dominant DGGE banding sequence was build, and the groups of the main indigenous bacteria was also analyzed. The result showed that the structure and the quantity of stratal microorganism indicated obvious differences, under different pressure conditions. The species number of dominant microbial population increased, and the structure of dominant microbial population obviously changed after activation. Before activation, the main bacteria were belonged to Bacillales, and after injecting activation agent, the species of Proteobacteria increased.