Flacherie in silkworms is defined as a state of larval health typified by flaccid condition of the affected larvae and caused by non-occluded viruses and bacteria individually and in combination. Among the silkworm diseases, flacherie is one of the major contributing factors to cocoon crop loss in India. The present work aims to isolate pathogens responsible for inflicting bacterial infection in Bombyx mori and characterize the associated bacteria. Mid gut contents were dissected from the larvae exhibiting typical symptoms of flacherie. The same were subjected to serial dilution and plated onto nutrient agar plates. Five bacterial cultures were isolated in axenic form and identity of the same was affirmed by sequencing the 16S rRNA gene. EZ Taxon BLAST analysis revealed that they were exhibiting highest sequence similarity to Staphylococcus argenteus, Paracoccus niistensis, Bacillus carboniphilus, Enterococcus cecorum and Enterobacter asburiae. Staphylococcus argenteus and Bacillus carboniphilus were found to be pathogenic to silkworm and inflicted mortality up to a tune of 50%.