Abstract: Background and Objective: Flies can be mechanical vectors of food borne enteric pathogenic bacteria. In Bangladesh, data on drug resistant fly associated bacteria is limited. Therefore, this study aimed to investigate the presence of drug resistant pathogenic bacteria in common flies found in Bangladesh. Methodology: Bacterial and fungal loads on the internal and external parts of common flies: Musca domestica and Lucilia sericata were enumerated through serial dilution and plating on nutrient agar and selective media. Biochemical tests were performed to identify bacteria, with further confirmation by 16S rRNA sequencing and BLAST search. Antibiogram of the isolated bacteria was performed by disk diffusion method. Results: The average count of bacteria from the fly external surface on the nutrient agar was 1.5×104 CFU mL–1for M. domestica and 1.6×106 CFU mL–1 for L. sericata. On the other hand, the average count of bacteria from the fly internal parts was 6.5×105 CFU mL–1 for M. domestica and 1.1×105 CFU mL–1 for L. sericata. Number of fungal colonies associated with the internal parts of the house fly (M. domestica) was 3.3×104 CFU mL–1 and of the green bottle fly (L. sericata) was 4.3×104 CFU mL–1. Salmonella typhimurium, Citrobacter, E. coli, Providencia, Shigella, Staphylococcus aureus and Klebsiella pneumoniae were isolated from the external parts of both type of flies. From the internal parts of the flies Serratia marcescens, Bacillus, Salmonella and Enterobacter were identified. All the isolated organisms from external parts of fly body showed the highest antimicrobial resistance against amoxicillin (95%) followed by cefixime (80%), gentamicin (35%), ciprofloxacin (25%) and chloramphenicol (20%). Conclusion: High numbers of bacteria with multiple drug resistance phenotypes are associated with flies. Therefore, further study is needed to determine the range of pathogenic bacteria being spreaded by flies.