Houseflies are alleged reservoirs as well as vectors of human and animal pathogens, including bacteria, because they frequently have contact with animal excreta and decaying organic substances. The rapid adaptation process of ingested microbes in the insect gut may involve gene transfer, including antibiotic resistance determinants among different bacterial strains. Six hundred and fifty-seven (n = 657) houseflies were collected from hospices and were identified morphologically and genetically using the16S rRNA,CO1, andITS2barcoding genes. This study also characterized the bacterial communities harboured by the captured houseflies using 16S rRNA metabarcoding on the next-generation sequencing (NGS) platform and further sought to detect antibiotic resistance traits by using gene-specific PCR assays. Generated sequences for the targeted gene fragments matched withMusca domesticaand all the sequences were deposited to the GenBank database. The 16S rRNA metabarcoding analysis revealed that the most abundant phyla detected with variable abundance observed among all the houseflies wereProteobacteria, followed byFirmicutes, andBacteroidetes. Furthermore, the NGS data revealed the presence of multiple bacterial genera, includingProvidencia,Enterobacter,Dysgonomonas,Escherichia-Shigella,Klebsiella,Pseudomonas, andStreptococcus, which are known to harbour potentially pathogenic species of animals and humans. Antibiotic resistance genes detected from the housefly DNA in this study includedermB,tetA,blaSHV, andblaTEM. Moreover, these genes are associated with resistance to erythromycin, tetracycline, and beta-lactams antibiotics, respectively. The presence of bacterial pathogens and the detection of antibiotic resistance genes from the houseflies collected from the hospices indicates the possible health risk to patients in hospices and the surrounding community. Therefore, it is imperative to keep high standards of hygiene, food preparation, safety, and control of houseflies in hospices.