Water hyacinth pretreated with microwave‐assisted dilute acid was used for fermentation to produce hydrogen using four kinds of genetically modified bacteria for the first time in this study. The genes of several hydrogenase were over‐expressed in Enterobacter cloacae CICC10017 and Enterobacter aerogenes ATCC13408. Four recombinant strains including E. cloacae/HPP, E. aerogenes/HycE, E. aerogenes/HycG, and E. aerogenes/HoxEFUYH were obtained. Hydrogen yields from water hyacinth were investigated, which were enhanced using the recombinant strains. When water hyacinth was pretreated by microwave at 140°C for 15 min with 1% H2SO4 and then hydrolyzed by cellulase, the reducing sugar yield of 49.4 g/100 g hyacinth was 91.4% of the theoretical reducing sugar yield. Among the four genetically modified bacteria, E. cloacae/HPP gave the highest hydrogen yield of 74.9 mL/g‐ total volatile solids, which was 50% higher than that given by the wild strain from pretreated water hyacinth. © 2017 American Institute of Chemical Engineers Environ Prog, 36: 1296–1300, 2017