BACKGROUND: Much research has been done on biochemical methane potential (BMP) determinations. However, although anaerobic digestion for methane production is driven by microorganisms, little information is available on the microbial community response to different organic residues. The aim of this study was to characterize the microbial communities during the treatment of different organic matrices. RESULTS: BMP were comparable for energy crops and several agro-industrial biomasses. Denaturing gradient gel electrophoresis (DGGE) showed the dominance of clostridia and Methanosarcina. Principal component analyses of PCR-DGGE profiles indicated microbial shifts between the start and end of the processes. Microbial communities showed similar structures that, in particular for Archaea, clustered together independently of the nature of the matrix treated. Bacterial communities were richer, more dynamic and even than archaeal ones. Real-time quantitative PCR revealed that the Methanosarcinales dominated the archaeal community while sulphate-reducing bacteria were present at low titers. A statistically significant correlation indicated that more even archaeal communities were associated with higher BMP. CONCLUSION: Different shifts occurred between Archaea and Bacteria exposed to different matrices treated by anaerobic digestion. While bacterial communities varied relatively widely, convergent archaeal community structures were selected in response to different biomasses treated. Copyright (c) 2012 Society of Chemical Industry