Abstract: In spite of its socio-economic and cultural importance to silk production, not much work has been done on Bombyx mori and silk farming in Nigeria. Of particular interest to this study is bacterial flacherie which is probably the most serious disease of Bombyx silkworm. Using a completely randomized block design, moribund (manifesting symptoms of flacherie disease) and dead larvae of three genetically distinct strains of silkworm and their runts were microbiologically analyzed for the presence of pathogenic bacteria on their body surfaces, gut and whole body. Standard Plate Count (SPC) was done by spread plate method. Bacteria isolation was done using standard microbiological procedures while identification of isolates was done using cultural, morphological and biochemical characteristics. Results show that Akure-China strain consistently showed the highest bacteria count regardless of the location of the insect body from which the sample was taken while the hybrid strain showed the lowest SPC values. The bacterial species isolated from the insect samples in this study were identified as follows: Bacillus badius, Citrobacter freundii, Citrobacter amalomaticus, Enterobacter cloacae, Staphylococcus epidermidis and Serratia marcescens. Results from the present study confirms the superiority of individuals of the hybrid strain to the Akure-China and the Akure-Japan strain when evaluated for their ability to prevent multiplication of pathogenic bacteria, an essential requirement for resistance to infection. Although, flacherie-causing organisms are present in the insect population, an outbreak will be avoided if proper hygiene is maintained by the farmers, ensuring that insects are reared under optimum conditions for productivity.