A time-course analysis was conducted of thermophilic anaerobic digestion of dairy manure and wheat distillery thin stillage. Sequencing of chaperonin targets provided a phylogenetic survey of both bacteria and archaea in the digestate, along with an appraisal of the diversity of the reactor microbiome. A total of 1129 bacterial operational taxonomic units (OTU) were detected in the reactors, with OTU related to Clostridium becoming numerically dominant by day 7, and Acetivibrio-related OTU by day 35. Archaeal communities were less diverse, with 19 OTU detected representing both acetoclastic and hydrogenotrophic methanogens. Regardless of input material, the same organisms came to dominate the reactors, reflecting strong selective pressures present in the digesters. Principal coordinate analysis of the microbial communities showed that the bacterial communities clustered based on factors other than input material. Bacterial and archaeal 011.1 were identified with significant correlations to performance parameters, suggesting important roles in the methane production pathway. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved.