The bacterial communities in three continuously stirred tank reactors co-digesting cow manure with grass silage. oat straw, and Sugar beet tops, respectively, were investigated by 16S rRNA gene-based fingerprints and clone libraries. The analyses revealed both clearly distinct and similar phylotypes in the bacterial communities between the reactors. The major groups represented in the three reactors were Clostridia, unclassified Bacteria, and Bacteroidetes. Phylotypes affiliated with Bacilli or Deltaproteobacteria were unique to the sugar beet and straw reactor, respectively. Unclassified Bacteria dominated in sugar beet reactor while in the straw and grass reactor Clostridia was the dominant group. An increase in organic loading rate from 2 to 3 kg volatile solids m (3) d (1) resulted in larger changes in the bacterial community in the straw compared to grass reactor. The study shed more light on the evolution of bacterial community during anaerobic co-digestion of different crops and manure to methane. (C) 2008 Elsevier Ltd. All rights reserved.