This study investigated the stimulating or inhibitory effect of Zn, Cu, Cd, Pb, and their mixtures on fermentative hydrogen production. Heavy metals inhibited the production process at all concentrations except 0.50 ppm of Zn. Consistent with the half of the maximum inhibitory concentration (IC50), Cu + Pb caused the greatest inhibition as it is more toxic than other heavy metal mixtures. As the concentration of heavy metal increased, the HBu/HAc ratio (butyrate/acetate) tended to decrease and the amount of hydrogen production decreased. Clostridium sp., Klebsiella sp., Dysgonomas sp., Enterobacter sp., and other hydrogen-producing bacteria were observed by polymerase chain reaction (PCR) – analysis by denaturing gradient gel electrophoresis (DGGE) during the fermentative hydrogen process. A significant relationship was observed between the richness index and the hydrogen production (p-value = 0.01 < 0.05) from the Pielou index. The Pielou index (E′) and the Shannon-Weaver index (H’) had no significant relationship (p-value = 0.12 > 0.05).