This study aims to identify bacteria isolated from the body surface of house flies from various habitats using 16S rRNA molecular barcodes. Houseflies were isolated from forests, hospitals, traditional markets, modern markets and landfills. 25 house flies isolated in each habitat. House flies were preserved in sterile bags. Bacterial isolation was carried out using nutrient agar media in 100 mm Petri dishes. The isolates obtained were pure cultured until a single isolate was obtained. Single isolates were extracted using Geneaid’s Presto TM Mini gDNA Bacteria Kit. The extracted bacterial total DNA was used as a template for amplification using primer 16s rRNA gene by PCR method. Nucleotide sequencing uses Singapore’s First BASE sequencing service. The results showed that single-house fly isolates from the Fish Auction (P.L.) showed a 99.11% similarity with Sphingobacterium faecium [CP094931.1]. Traditional market bacterial isolates (P.T.) showed 97% similarity with Pseudochrobactrum sp. XF203. Hospital bacterial isolates (R.S.) showed 99.11% similarity with S. faecium [CP094931.1]. Bacterial isolates from residential areas (PM) showed 99% similarity with Brucella abortus RB51-AHVLA. Bacterial isolates from the forest (H.T.) showed 94% similarity with Bacillus paralicheniformis [CP043501.1]. There are associated bacteria that are used as biotechnology agents. Exploration of bacteria and even microbes associated with M. domestica is still extensive to be studied in the future.