Microbial electrolysis cells (MECs) use exoelectrogenic microorganisms to convert organic matter into H-2, although yields can vary significantly with environmental conditions, likely due to variations in microbial communities. This study was undertaken to better understand how microbial communities affect reactor function. Using wastewater as inoculum, 15 MEC reactors were operated for >50 days and subsequently five reactors were selected for further analysis. Solution (26 mL) was collected every 3-4 days for DNA extraction. DNA was hybridized to GeoChip, a comprehensive functional gene array, to examine differences in the reactor microbial communities. A large variety of microbial functional genes were observed in all reactors. Performances ranged from poor (0.1 +/- 0.1 mL) to high (12.2 +/- 1.0 mL) H-2 production, with a maximum yield of 5.01 +/- 0.43 mol H-2/mol(glucose). The best performance was associated with higher cytochrome c genes, considerably higher exoelectrogenic bacteria (such as Shewanella, Geobacter), less methanogens and less hydrogen-utilizing bacteria. The results confirmed the possibility to obtain an effective community for hydrogen production using wastewater as inoculum. Not like fermentation, hydrogen production was significantly controlled by electron transporting process in MECs. GeoChip findings suggested that biofilm formation can be highly stochastic and that presence of dissimilatory metal-reducing bacteria and antagonistic methanogens is critical for efficient hydrogen production in MEC reactors. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.