This study was designed to evaluate a treatment system for high strength wastewater (vinasse) from a sugarcane molasses-based bio-ethanol plant in Thailand. A laboratory-scale two-phase treatment system composed of a sulfate reducing (SR) tank and multi-staged up-flow anaerobic sludge blanket (MS-UASB) reactor was used as the pre-treatment unit. Conventional UASB and down-flow hanging sponge (DHS) reactors were used as the post-treatment unit. The treatment system was operated for 300 days under ambient temperature conditions (24.6-29.6 °C). The hydraulic retention time (HRT) in each unit was kept at 25 h for the two-phase system and 23 h for the UASB&DHS. The influent concentration was allowed to reach up to 15,000 mg chemical oxygen demand (COD)/L. COD removal efficiency (based on influent COD) of the two-phase MS-UASB and the UASB&DHS was 54.9 and 18.7%, respectively. Due to the effective removal of sulfide in the SR tank, the MS-UASB achieved a high methane conversion ratio of up to 97%. In DHS, nitrification occurred at the outside portion of the sponge media while denitrification occurred at the inside. Consequently, 27% of the total nitrogen (TN) was removed. An amount of 32% of residual nitrogen (28 mgN/L) was in the form of nitrate, a better nitrogen state for fertilizer.