Irritable bowel syndrome (IBS) is a common gastrointestinal condition whose cause remains unknown. Therefore, most of our effort in treating IBS has been based on a symptom approach. Recent evidence is beginning to suggest that subjects with IBS may have an alteration in gastrointestinal flora. Specifically, findings suggest that IBS patients have excessive bacteria in the small bowel, known as bacterial overgrowth. Although diagnostic testing for bacterial overgrowth is somewhat controversial, as there is no true gold standard test for bacterial overgrowth, antibiotic-based therapies for IBS are now shown to be very effective in treating IBS. Follow-up work in this area has even begun to demonstrate associative factors between gut bacteria and IBS that may explain the different types of IBS. The best example of this is the finding that methanogenic organisms in IBS patients are wholly associated with constipation-predominant IBS. It seems that the methane gas emitted during fermentation may have an influence on gut motility. In this review, the evidence for gut ecology associations in IBS is presented. A treatment algorithm also is proposed based on these findings. New areas of research in IBS such as gut bacteria are changing the treatment approach in IBS from a symptom-based style to one that is hypothesis driven.