Hydrogen(H-2)-producing bacterial community structures of the dark fermentation system in a batch reactor were investigated during 48 h by analyzing 16S rRNA gene sequences obtained from pyrosequencing. Organic wastes composed of food waste and sewage sludge were used as a feedstock. After heat treatment (90 degrees C for 20 min) of the feedstock, H-2 was naturally evolved under anaerobic mesophilic conditions, showing a H-2 yield of 2.26 mol H-2/mol hexose(added). The bacterial community structure of the initial inoculum (microbial community at the starting point (0 h)) combined with heat treated food waste and sewage sludge was mainly comprised of Proteobacteria and Bacteroidetes. After 6 h operation, the sequences that belong to other groups except Firmicutes decreased dramatically and were not observed at all in the latter samples. Clostridium spp., which were negligible in the inoculum, took over the main bacterial community by taking charge of H-2 production. Among the phylum Firmicutes, the sequences closely related with Clostridium sordellii ATCC 9714(T), Clostridium perfringens ATCC 13124(T), and Clostridium butyricum ATCC 19398(T) became predominant in the time series within 48 h. Overall, the results showed how fast the Clostridium spp. overwhelmed the bacterial community in dark fermentative H-2 production conditions, where they were at a negligible amount at the start. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.