We compared the microbial community structures that developed in the biofilm anode of two microbial electrolysis cells fed with ethanol, a fermentable substrate-one where methanogenesis was allowed and another in which it was completely inhibited with 2-bromoethane sulfonate. We observed a three-way syntrophy among ethanol fermenters, acetate-oxidizing anode-respiring bacteria (ARB), and a H-2 scavenger. When methanogenesis was allowed, H-2-oxidizing methanogens were the H-2 scavengers, but when methanogenesis was inhibited, homo-acetogens became a channel for electron flow from H-2 to current through acetate. We established the presence of homo-acetogens by two independent molecular techniques: 16S rRNA gene based pyrosequencing and a clone library from a highly conserved region in the functional gene encoding formyltetrahydrofolate synthetase in homo-acetogens. Both methods documented the presence of the homo-acetogenic genus, Acetobacterium, only with methanogenic inhibition. Pyrosequencing also showed a predominance,of ethanol-fermenting bacteria, primarily represented by the genus Pelobacter. The next most abundant group Was a diverse community of ARB, and they were followed,by H-2-scavenging syntrophic partners that were either H-2-oxidizing methanogens or homo-acetogens when methanogenesis was suppressed. Thus, the community structure in the biofilm anode and suspension reflected the electron-flow distribution and H-2-scavenging mechanism. Biotechnol. Bioeng. 2010;105: 69-78. (C) 2009 Wiley Periodicals, Inc.