Anaerobic treatment of cane-molasses alcohol stillage was studied in a thermophilic two-phase system comprising two bioreactors for the acidogenic and methanogenic phases respectively in comparison with the single-phase process. The experiments were conducted with HRT ranging from 36.0 to 9.0 days for single-phase and from 32.7 to 5.6 days for two-phase, corresponding to organic loading rates of 3.452 to 14.487 and 4.646 to 20.022 kgCODm−3day−1 respectively. The treatment efficiency was essentially maintained at BOD5 and COD removal of over 85% and 65% respectively in the two-phase process even with higher substrate loading. The acidogenic phase provided satisfactory conversion of initial COD to VFA averaging 15.6% in the degree of acidification. The methanogenic culture pH of both systems was maintained in a range of 7.4 to 7.8 through self regulation. The methane content of the biogas generated from the two-phase process was significantly higher by about 17% than that from the single-phase process, both decreasing with increasing substrate loading and shorter HRT. The mean overall methane yield was found to be 0.168 m3CH4(STP)kg−1 CODadded or 0.292 m3CH4(STP)kg−1 VSadded from two-phase methanogenesis, compared to 0.055 m3CH4(STP)kg−1CODadded or 0.082 m3CH4(STP)kg−1VSadded from single-phase fermentation. However, methane yield in the two-phase process was enhanced only at COD loading rates higher than 2.9 kgm−3day−1 or VS loading rates higher than 1.8 kgm−3day−1. The ultimate methane yield was evaluated graphically to be 0.216 m3CH4(STP)kg−1CODadded, or 0.401 m3CH4(STP)kg−1 VSadded. This indicated a methane yield efficiency of 73-78% for the two-phase anaerobic digestion of cane-molasses alcohol stillage, which was composed of 24.2% and 28.2% of non-biodegradable COD and VS respectively. Kinetic evaluation of the experimental data provided θm (minumum SRT) and K (kinetic constant) values as 6.6 days and 0.166 respectively based on COD, or 7.0 days and 0.160 respectively based on VS. Application of the two-phase anaerobic process on full scale at an industrial treatment plant for alcohol stillage showed mean treatment efficiency in terms of BOD5 and COD reduction of 84.3% and 63.2% respectively at an average loading rate of 5.1 kgCODm−3day−1, which was in good agreement with the bench-scale studies, considering the great variation in the raw wastewater characteristics typical of an industrial operation.