Denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA gene clone library methods were used to analyze the microbial communities of a water injection well (G) and an oil production well (L) at two sampling time points (A and B) in Gudao block of Shengli oilfield. DGGE profile showed that the microbial similarity of sample G at two sampling time was 48.1%, that of sample L was 28.7%, respectively. Sequence analysis of 16S rRNA gene clone libraries showed that bacteria in G library at time point A were mainly Betaproteobacteria and Gammaproteobacteria, and also with low percentage of Deferribacteres, Firmicutes and Bacteroidetes; But in L library, 97% bacteria belong to Moraxellaceae of Gammaproteobacteria. Whereas, the main type of bacteria in sample G at time point B were Betaproteobacteria and Deferribacteres. The bacterial composition of sample L was dominated by Gammaproteobacteria, Betaproteobacteria and Firmicutes. Both DGGE and clone library indicated the distinct temporary shift of microbial communities of production well, but much less change happened in injection water sample. Our results will benefit to the better understanding of mechanisms of microbial enhanced oil recovery.