The efficiency and the methanogens composition in an upflow anaerobic sludge blanket (UASB) reactor and a continuous stirred-tank reactor (CSTR) are investigated after achieving steady states at the same organic loading rate (OLR) of 6.0 kg·m-3·d^-1. The results show that the average removal rate of COD reaches 95% in the UASB, significantly higher than 84% of the CSTR. However, the specific methane production rate and the specific COD removal rate of the activated sludge are 315 L·kg^-1·d^-1 and 0.85 kg·kg^-1·d^-1, respectively, in the CSTR, notably higher than those of the UASB of 260 L·kg^-1·d^-1 and 0.67 kg·kg^-1·d^-1, respectively. The analysis of the methanogens composition of the activated sludge by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) indicates that Methanosaeta concilii and Methanospirillum hungatei are the dominant methanogens in the UASB, while Methanosarcina mazeii and Methanobacterium formicicum are dominant in the CSTR. The diversity of the microbial community composition and the metabolic characteristics are the underlying reasons for the difference in the performance of the anaerobic treatment system. The UASB and the CSTR have their respective advantages in the COD removal or specific activities of the activated sludge. It is reasonable to choose a perfect bioreactor (UASB or CSTR) for a practical engineering based on the quality of the wastewater and the required extent of the treatment.