The present study investigated the shifts in the chemical profiles of a two-phase anaerobic digestion system in methanogenic and acidogenic reactors for the treatment of swine wastewater. Acidogenic and methanogenic digesters were used with overall HRTs ranging from 27 to 6 d. In the optimized thermophilic/acidogenic phase throughout the entire experimental period, VS was reduced by 13.8% (1.6%); however, COD hardly decreased because of the thermophilic hydrolysis of organic materials, such as carbohydrates, proteins, and lipids, without any significant consumption of volatile fatty adds. In the methanogenic/mesophilic phase, COD was reduced by 65.8 (1.1)% compared to a 47.4 (2.9)% reduction in VS reduction efficiency with the gradual increase in methane production during a methanogenic HRT between 25 and 10 d. A high protein degradation rate was observed in the optimized acidogenic phase, which is assumed to be due to the low content of carbohydrates in raw swine wastewater as well as the readily thermophilic hydrolysis of proteins. Two-phase systems of anaerobic digestion consisting of optimized thermophilic and mesophilic methanogenic digesters showed a stable performance with respect to VS reduction efficiency with OLRs less than 3 g VS/L.d, in other words, more than 10 days of methanogenic HRT in this study. (C) 2012, The Society for Biotechnology, Japan. All rights reserved.