A diverse range of effects of the intestinal microbiota on mucosal defence and injury has become increasingly clear over the past decade. Hydrogen sulfide (H2S) has emerged as an important mediator of many physiological functions, including gastrointestinal mucosal defence and repair. Hydrogen sulfide is produced gastrointestinal tract tissues and by bacteria residing within the gut, and can influence the function of a wide range of cells. The microbiota also appears to be an important target of hydrogen sulfide. H2S donors can modify the gut microbiota and the gastrointestinal epithelium is a major site of oxidation of microbial-derived H2S. When administered together with nonsteroidal anti-inflammatory drugs, H2S can prevent some of the dysbiosis those drugs induce, possibly contributing to the observed prevention of gastrointestinal damage. Exogenous H2S can also markedly reduce the severity of experimental colitis and plays important roles in modulating epithelial cell-mucus-bacterial interactions in the intestine, contributing to its ability to promote resolution of inflammation and repair of tissue injury. In this paper we review recent studies examining the roles of H2S in mucosal defence, the possibility that H2S can damage the GI epithelium, effects of H2S on the gut microbiota and on mucus and biofilm interactions in the context of intestinal inflammation.