House flies (Musca domestica L.) and green flies (Chrysomya megachepala L.) are two species of flies that are vectors of many types of bacteria in humans and animals throughout the world. The research was conducted to determine the sequence of the 16S rRNA gene and thus to conduct the phylogenic position, the bacteria isolated from Musca domestica and Chrysomya megachepala L used the 16S rRNA gene as a barcode. The bacteria identified were bacteria that have been tested to produce antibiotics. Pure cultures of each of the seven bacterial isolates were used for DNA analysis dan molecular identification. The results showed that the S1 isolate had a 90% similarity with the Bifidobacterium minimum [NR 044692.2]. Isolate S2, showing similarity of 86% with Alcaligenes faecalis [CP021883.1]. Isolate S3 has similarty 94% Brucella melitensis bv. [NR_076080.2]. Isolate S4 has a similarity of 99% with Sphingobacterium sp. [LK931720.1]. Isolate S5 has a similarity of 100% with Bacillus sp. [MH071158.1]. Isolate S6 has a similarity of 97% with Gamma proteobacterium [KJ127178.1]. While isolate S7 has a similarity of 100% Enterobacter asburiae [MH071322.1]. Species of bacteria identified from green flies and house flies that inhabit the city of Luwuk have never been reported to be associated with flies.