Microbiota as an effective part of gut mucus plays an important role in the maintenance of gut integrity and homeostasis. Alterations of gut-microbiota profile by increasing the abundance of pathogenic-bacteria and reducing the beneficial-bacteria, are associated to colorectal adenomas (CRA) and cancer (CRC). Pathogenic-bacteria can induce chromosomal instability and gene mutations in bowel cells, disrupt intestinal barrier and affect the function of immune cells. These modifications might be responsible for the intestinal inflammation, tissue damages and tumorigenesis. The use of antibacterial elements such as selenium (Se), might have a modulating effect on composition and function of microbiota. This study discusses the mechanisms of effect of selenium on microbiota in CRC. Relevant studies in electronic databases were selected by searching MEDLINE Library. Available studies suggested that selenium might influence on microbiota in CRC through multiple pathways. As the Se metabolites or part of selenoproteins, Se reduces incidence of CRC by regulation of immune cells functions, and decrease of oxidative stress. About one quarter of gut microbiota use Se for the expression of selenoproteins, and therefore decrease the availability of Se for host selenoproteins. In addition, in Se deficiency, pathogenic-bacteria are elevated and transport of Se to host tissues and organs are reduced by down-regulation of selenoprotein P. However, Se supplementation could increase probiotic-microbiota, ratio of beneficial to pathogenic-bacteria and quantity of butyric acid as an energy source of colonocytes where develop intestinal morphology and villus height for improvement of capacity of nutrients absorption. In addition, Se increases bacterial fermentation products such as short chain fatty acids, which improve the immune responses, epithelial tight junctions, gut integrity, mucosal functions, control bacterial pathogenesis, inhibit inflammation and carcinogenesis and decrease oxidative stress. In sum, Se may protect against colorectal cancer by modulation of probiotic bacteria, improvement of intestinal morphology and increase in bacterial fermentation.