To explore of role of microbial diversity and its functionality in commercial bioreactors, three anaerobic microbial communities from Ontario, Canada were characterized using 16S rRNA gene-based, clone library sequencing and terminal restriction fragment length polymorphism (T-RFLP) and compared with the hydrogen (H-2) and methane yields. The T-RFLP method showed more operational taxonomic units than the clone library sequence analysis; however, the two methods showed similar dominant species and relative diversity while Spearman's Rank correlation coefficient (r) values ranged from 0.82 to 0.91. The Chao 1 and Shannon-Wiener indices revealed that the cultures samples have highly diverse microbial communities. Comparatively, cultures from a municipal wastewater treatment plant (CA) showed more diversity than those from facilities treating effluents from a baby food processor and a brewery. Even though culture CA has the highest microbial diversity, low H-2 and methane production yield was attributed to the presence of sulphate reducers, propionate producers and a low percentage of methanogens. This study confirms that the selection of the source of mixed anaerobic cultures plays an important role in H-2 and methane production. Crown Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.