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Abstract Insecticide resistance has emerged as a persistent threat to the fight against vector-borne diseases. We compared the gut microbiota of permethrin-selected (PS) strain ofAedes aegyptirelative to the parent (KW) strain from Key West, Florida. Bacterial richness but not diversity was significantly higher in PS strain compared to KW strain. The two mosquito strains also differed in their gut microbial composition.Cutibacteriumspp.,Corynebacteriumspp.,Citricoccusspp.,Leucobacterspp.,Acinetobacterspp.,Dietziaspp., andAnaerococcusspp. were more abundant in PS strain than in KW strain. In contrast,Sphingomonasspp.,Aquabacteriumspp.,Methylobacteriumspp.,Flavobacteriumspp.,Lactobacillusspp., unclassified Burkholderiaceae and unclassified Nostocaceae were more abundant in KW strain compared to PS strain. PS strain was enriched with propionate metabolizers, selenate reducers, and xylan, chitin, and chlorophenol degraders while KW strain was enriched with sulfur oxidizers, sulfur metabolizers, sulfate reducers and naphthalene and aromatic hydrocarbons degraders. These findings demonstrate an association between the gut microbiota and insecticide resistance in an important vector species and sets the foundation for future studies to investigate the contribution of gut microbiota to evolution of insecticide resistance in disease vectors.