The objective of the current study is to investigate the bacterial colonization within the gut of the house fly, Musca domestica L. (Diptera: Muscidae), at the larval stage and the bacterial community of the gut of the house fly at the newly emerged adult stage. After using ethidium monoazide to inhibit recovery of nucleic acids from dead bacteria, three polymerase chain reaction (PCR)-amplified 16S rDNA libraries from wheat bran, larvae, and newly emerged adults was constructed, analyzed, and compared. In total, 24, 11, and four phylotypes in the 16S rDNA libraries of wheat bran and the gut of larvae and adults, respectively, were found and assigned to three phylogenetic phyla of the domain Bacteria: Firmicutes, Proteobacteria, and Bacteroidetes. In the wheat bran library, 76% of the total number of sequences were affiliated to the genera Pseudomonas, Halomonas, Providencia, and Ignatzschineria. The three genera Morganella (79.05%), Providencia (8.78%), and Ignatzschineria (9.46%) dominated the library of the larval gut. Compared with the wheat bran library, the relative abundance of Morganella morganii (Winslow) was significantly higher (79.05 versus 0.8%), whereas that of Ignatzschineria larvae and of Providencia spp. was similar. These results demonstrate that M. morganii, Providencia spp., and I. larvae colonized the gut of the house fly larvae. Live bacteria of M. morganii, Providencia spp., and Proteus spp. were found in the gut of newly emerged adults. Therefore, the bacteria M. morganii and Providencia spp. colonized the larval gut could survive in the gut from larval metamorphosis to adult eclosion of the house fly.