Functional bowel disorders (FBDs) are functional gastrointestinal disorders with symptoms attributable to the middle or lower gastrointestinal tract. These include irritable bowel syndrome, functional bloating, functional. constipation, functional diarrhea, and unspecified FBD. Increasing evidence has emerged of late that intestinal microbiota is involved in the pathogenesis of FBDs. In this review, the therapeutic benefits and future perspectives of the currently available strategies for modifying the gut microbiota in FBDs are described, focusing primarily on irritable bowel syndrome and functional constipation.