Trillions of microbes inhabiting the intestine form a complex ecological community, affecting the normal physiology and pathological susceptibility through their collective metabolic activities and interactions with the host. Increased numbers of diseases have been found to be associated with disturbances in this ecosystem. There is evidence that intestinal microflora undergoes alterations in patients with irritable bowel syndrome (IBS). IBS is a frequent functional gut disease with negative impact on the patient's quality of life. Although the etiology and pathology of IBS remain largely unknown, it is generally accepted that the interaction between the microbiota and the host is associated with IBS. However, there are no specific or effective therapies for the treatment of IBS at present. In recent years, researchers have shown a growing interest in seeking safer and more effective alternatives for the treatment of IBS by focusing their attention on the potential role of probiotics and prebiotics. In this review, we will discuss alterations in intestinal microbiota and how these alterations may exacerbate IBS, and introduce several new IBS treatment options aiming at re-establishing a healthy and beneficial ecosystem.