The [NiFe]-hydrogenase 3 of Enterobacter aerogenes contains a large subunit of 60 kDa (HycE) and a small subunit of 30 kDa (HycG). The gene of HycE and the gene of HycG were overexpressed in E. aerogenes separately by using the pGEX-4T-2-cat vector, to obtain two recombinant strains: E. aerogenes/HycE and E. aerogenes/HycG. The hydrogen yields were significantly enhanced by the recombinant strains. The hydrogenase activities of the recombinant strains increased by 124% (E. aerogenes/HycE) and 67% (E. aerogenes/HycG) compared with that of the wild strain. The hydrogen yields of the recombinant strains from initial glucose increased by 86.2% to 2.16 mol H2/mol (E. aerogenes/HycE) and by 69.8% to 1.97 mol H2/mol (E. aerogenes/HycG). The recombinant strains produced more acetate and butyrate than the wild strain, and this finding corresponded to the metabolism of NADH.