Gut microbiota play several physiological and pathophysiological roles. Dysbiosis, a state of altered gut microbiota, has been increasingly recognized for its association with various diseases. In line with this trend, functional bowel disorders, which are disorders of gut-brain interaction in the lower gastrointestinal tract, are influenced by gut microbiota. As treatments of functional bowel disorders targeting gut microbiota include probiotics, low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diets, non-absorbable antibiotics, and fecal microbiota transplantation are known. However, the optimal treatment strategy in this area is not established yet. Further research is required to investigate these issues.