The human gut consists of many microorganisms. The exact components of bacteria are undetermined, but studies based on molecular analysis have revealed that there are two main of phyla, Firmicutes and Bacteroidetes. The gut microbiota has been appeared to participate in specific metabolic activities. Disruption of normal gut microbiota (dysbiosis) is associated with systemic and metabolic disease, such as chronic kidney disease (CKD). Recent studies revealed quantitative and qualitative changes in gut microbiota in patients with CKD. In addition, dysbiotic gut microbiome may participate in progression CKD and CKD associated complications. Investigation determined dietary habit in short- or long-term is one of the most important factors that influence the diversity and constitution of the human intestinal microbiota thus, affecting host metabolism and disorder risk or progress. In addition, increased interest has created in using probiotics, and prebiotics to decrease the risk of dysbiosis in the intestinal to prevent or cure the human illnesses. In this review we summarized the gut microbiota composition, the relation between gut microbiota and CKD, and dietary factors that influence on gut microbiota and finally we concluded that the Mediterranean diet with probiotic, prebiotic or symbiotic direction are ideal and innovative method for CKD patients.