Many bacteria reduce inorganic sulfate to sulfide to satisfy their need for sulfur, one of the most important elements for biological life. But little is known about the metabolic pathways involving hydrogen sulfide (H2S) in mesophilic bacteria. By genomic sequence analysis, a complete set of genes for the assimilatory sulfate reduction pathway has been identified in the ethanologen Zymomonas mobilis. In this study, the first ATP sulfurylase- and final sulfite reductase-encoding genes cysND and cysIJ, respectively, in the putative pathway from sulfate to sulfite in Z. mobilis ZM4 was singly or doubly inactivated by homologous recombination and a site-specific FLP-FRT recombination. The resultant mutants, ∆cysND, ∆cysIJ and ∆cysND-cat∆cysIJ, were unable to produce detectable H2S in glucose or sucrose-containing rich medium and sweet sorghum juice, in which the wild-type ZM4 produced detectable H2S. While adding sulfite (SO3 2−) into media impaired the growth of the mutants and ZM4 to varying degrees, the sulfite restored the H2S formation in the ∆cysND in the above media, but not in the ∆cysIJ and ∆cysND-cat∆cysIJ mutants. Although it seemed that the inactivation of cysND and cysIJ did not exert a significant negative effect on the cell growth at least in glucose or sucrose medium, the ethanol production of all mutants was inferior to that of ZM4 in sucrose medium and sweet sorghum juice. In addition, adding l-cysteine to glucose-containing rich media restored H2S formation of all mutants, indicating the existence of another pathway for producing H2S in Z. mobilis. All these results would help to further elucidate the metabolic pathways involving H2S in Z. mobilis and exploit the biotechnological applications of this industrially important bacterium.