Microbial community structure and dynamics were examined in two anaerobic reactors run in repeated-batch mode to treat whey permeate. Despite being started up using different seeding sources, the reactors showed generally similar reaction patterns and performances. During the repeated-batch operation for three cycles, the overall reaction rate increased with the increase in the initial population size of both bacteria and methanogens over cycles. Clostridium- and Methanospirillum-related microorganisms were likely the main acidogenic and methanogenic populations, respectively, in both reactors. Bacterial community structure shifted dynamically over cycles, while little change was observed in methanogen community structure throughout the operation. This means that the changes in bacterial community structure changes had little influence on the formation and evolution of methanogen community structure in the reactors. The increased methanogenesis rate with cycles seemed therefore more likely due to the effect of the increase in methanogen abundance rather than the alteration of community structure. (C) 2012 Elsevier Ltd. All rights reserved.