Food waste leachate (FWL) from the food waste recycling facilities in Korea is a serious environmental problem. Much research was done on anaerobic digestion of FWL in a lab-scale; however, there is little information on a large scale anaerobic digestion system (ADS). In this study, a two-phase ADS in a pilot scale was operated using FWL and the ADS performance and microbial structure dynamics using pyrosequencing were investigated. The ADS was operated for 136 days using FWL containing a high concentration of volatile fatty acid (12,435 +/- 2203 mg/L), exhibiting volatile acid (VS) removal efficiency of 74-89% and CH4 yield of 0.39-0.85 Nm(3)/kg of reduced VS. The microbial structure at 76, 101, and 132 days indicated the methanogen population shift from acetoclastic methanogens (Methanosarcina and Methanosaeta) to hydrogenotrophic methanogens (Methanobacterium and Methanoculleus). The bacterial community also shifted to the taxa syntrophically related with hydrogenotrophic methanogens (Clostridia). The statistical analysis revealed the positive correlation of VS removal efficiency with Methanosarcina, but the negative correlation with Methanobacterium. The results presented here suggest that acetoclastic methanogens and their associated bacteria were more efficient for VS removal in the pilot scale ADS system, providing useful information for FWL treatment in a large scale ADS. (C) 2013 Elsevier Ltd. All rights reserved.