The alkane-degrading bacterium and methanogenic were the important functional populations in oil reservoirs and their diversities were investigated by FISH and DGGE, respectively. The DGGE profiles showed great difference between the alkB genes in samples. And the major bands detected in injection wells were obviously more than them in production wells. The FISH results indicated that the quantity of archaea was much more than bacteria in the samples and they had close spatial distribution in situ. The results indicated that alkane-degrading bacterium and methanogenic populations were diverse in oil reservoirs and formed compact aggregates in situ. The incubation of Shengli oilfield production water degraded more than 50% residual oil during 130 d culture, with the production rate of methane reaching up to 1.57×10^?2 mmol/(L?d). Molecular analysis of the functional populations of microbial community in oilfield will provide the information for better application of microbial enhanced oil recovery.