The effects of heavy metals on fermentative hydrogen production were examined based on metal type and concentration. Hydrogen production was stimulated by low concentrations of Cd and Zn but decreased at concentrations of 40 and 1 mg/L, respectively. Hydrogen production was inhibited for the entire range of Cu tested. The order of toxic density was Cu > Zn > Cd at concentrations below 2 mg/L but was Zn > Cu > Cd at higher concentrations. The depression rates of hydrogen production were calculated to be 225.8 mL-H 2/mg-Zn, 67.37 mL-H 2/mg-Cu, and 13.39 mL-H 2/mg-Cd. The presence of heavy metals caused a shift in microbial community. The presence of Clostridium genus bacteria, identified as Clostridium magum, Clostridium diolis, and Clostridium sp., resulted in active hydrogen production. Klebsiella genus bacteria were the most abundant of the class Gammaproteobacteria and also stimulated hydrogen production at relatively low concentrations of heavy metal. When Rhodocista pekingensis, Erwinia chrysanthemi strain 1015-1, Delftia sp. YF 31, or uncultured Klebsiella sp. clone F1 apr.32 were present, hydrogen production was seriously decreased.