Gut microflora of insects are implicated in many physiologically important systems in insects like host nutrition, semiochemical production, detoxification of toxic metabolites and colonization resistance to invading pathogens. Studies have shown that gut microbes play an active role in resisting the invading pathogens through production of antibacterial metabolites and physiological changes in gut environment to prevent colonization of bacteria other than the indigenous ones. By using a molecular marker (kanamycin resistance) tagged test bacterial strain, Escherichia coli, studies have been conducted to prove colonization resistance of gut microflora to invading microbes in silkworm Bombyx mori L. Under selective conditions of Gnotobiotic (limited gut microflora) silkworm and probiotics application of S. noursei, temporal dynamics of colonization pattern of molecular marker tagged E. coli was tracked to establish colonization resistance of gut microflora to invading pathogens.