In this research, a study of anaerobic digestion to generate methane in anaerobic sequencing batch reactor (ASBR) were conducted in a single stage system (using raw sago mill effluent (SME) as substrate) and two stage system (using acidogenic effluents from hydrogenic reactor treating sago mill effluent) operated under mesophilic condition. The experiment was carried out over a range of hydraulic retention times (HRT) of 12 to 1.5 days in both single and two stage system, respectively. The corresponding organic loading rate (OLR) was 1.21 to 9.90 kg COD/m3.d and 1.41 to 11.17 kg COD/m3.d, respectively. The performance of methane generation and organic matter degradation of these two systems were evaluated and compared. The highest methane production rate (MPR) and methane yield (MY) were obtained from the two-stage system under HRT 2 days at 1.7111 L CH4/Lreactor.d and 0.2257 L CH4/g CODremoved respectively with a maximum percentage of COD reduction of 82%. Meanwhile, single stage system operated under the same HRT obtained lower methane production rate at 1.254 L CH4/Lreactor.d and methane yield of 0.2217 L CH4/g CODremoved. Overall, this study demonstrated a two-stage system is able to provide higher methane productivity as compared to a single stage system.