Background: The ability of blood feeding arthropods to successfully acquire and transmit pathogens of medical and veterinary importance has been shown to be interfered or enhanced by the arthropod’s native microbiome. Mosquitoes transmit bacteria, viruses, protozoan and filarial nematodes, majority of which contributes to the 17% of infectious disease cases worldwide. Dirofilaria immitis, a mosquito transmitted filarial nematodes of dogs and cats, is vectored by several mosquito species including Aedes aegypti.Methods: In this study, we investigated the impact of D. immitis colonization on the microbiome of laboratory reared female A. aegypti. Metagenomic analysis of the V3-V4 variable region of the microbial 16SRNA was used for identification of the microbial differences down to species level.Results: We generated a total of 1068 OTUs representing 16 phyla, 181 genera and 271 bacterial species. Overall, in order of abundance, Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the most represented phylum with D. immitis infected mosquitoes having more of Proteobacteria (71%) than uninfected mosquitoes (56.9%). An interesting finding in this study is the detection of Klebsiella oxytoca in relatively similar abundance in infected and uninfected mosquitoes. It has been previously shown to indirectly compete for nutrients with fungi on the domestic housefly eggs and larva. While not statistically significant, D. immitis infection alters bacterial diversity by reducing the bacterial species richness and abundance.Conclusions: In conclusion, this is the first study to the best of our knowledge to understand the impact of a filarial infection on the microbiome of its mosquito vector. While the microbiome composition of A. aegypti mosquito have been previously reported, our study shows that in an effort to establish itself, a filarial nematode modifies and alters the overall microbial diversity within its mosquito host.