: The gut microflora of silkworm, Bombyx mori L. are associated with various physiological processes besides providing colonization resistance to invading pathogens through production of antimicrobial compounds. Characterisation of beneficial gut microbes finds wide application in commercial sericulture. Culture dependent techniques coupled with biochemical tests are tedious in characterizing heterogenous microflora. The tools of molecular biology offer novel techniques to characterize hitherto unculturable gut microflora. PCR probes based on 16S rRNA genes are widely used for detection and characterization of microbes. By using specific PCR probes with intervening sequences of 16S rRNA genes, molecular characterization of functionally important beneficial microbes viz., Bacillus subtilis, Pseudomonas fluorescens and Streptomyces noursei have been done from the gut of indigenous silkworm breeds in the present study.