An anaerobic baffled reactor (ABR) was employed to investigate the operational performance and the distribution of syntrophic methanogens during the treatment of sugar refinery wastewater. The distribution of syntrophic methanogens was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). COD removal was 61.5% and volatile fatty acids (VFAs) in effluent were 1808mg/L at sludge acclimation stage. After the regulation operation of two stages, the VFAs were dramatically reduced and methane content was increased to above 55%. The COD removal was achieved 94.8% at the stable state. The granular sludge with good settling performance was formed in the last 3compartments. PCR-DGGE explored that the dominant hydrogen-producing acetogens were related to the genera Syntrophobacter and Pelotomaculum, which were distributed in the third and fourth compartments of ABR. The acid-tolerant hydrogenotrophic methanogens (Methanoregula and Methanosphaerula) were mainly distributed in the first and second compartments, while acetotrophic methanogens (Methanosaeta and Methanothrix) mainly existed in the third and fourth compartments. The present study found the diversity of methanogens was higher than that of hydrogen-producing acetogens, indicating hydrogen-producing acetogenesis is more likely to be a rate-limiting step when the system is shocked.