Microorganisms coexist in the human body and its function is essential to maintain normal physiology and homeostasis. Microbiota refers to the entire population of microorganisms that colonizes a particular location; includes not just bacteria but also other microbes. Gut microbiota is vast and complex. It could be changed dynamically according to the variable factors. Well balanced host-microbial symbiotic state is a harmonious ecosystem in the stable individual. But, dysbiosis is a state of deviation in composition or function from the usual gut microbiota. It has been found that this condition is associated with many gastrointestinal, metabolic, allergic and the other diseases. Dysbiosis plays an important role in the pathophysiology of functional bowel disease, such as irritable bowel syndrome and functional constipation. Probiotics is microorganism which, when administrated in adequate amounts, confer a health benefit on the host. Probiotics have beneficial effects to reduce several symptoms of functional bowel diseases. Currently, complementary and alternative medicine therapies with probiotics is recommended for symptomatic relief from functional bowel disease.