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Epidemics of arboviruses in general, and dengue fever in particular, are an increasing threat in areas where <i>Aedes (Ae.) aegypti</i> is present. The effectiveness of chemical control of <i>Ae. aegypti</i> is jeopardized by the increasing frequency of insecticide resistance. The aim of this study was to determine the susceptibility status of <i>Ae. aegypti</i> to public health insecticides and assess the underlying mechanisms driving insecticide resistance. <i>Ae. aegypti</i> eggs were collected in two study sites in the vicinity of houses for two weeks using gravid <i>Aedes</i> traps (GATs). After rearing the mosquitoes to adulthood, female <i>Ae. aegypti</i> were exposed to diagnostic doses of permethrin, deltamethrin and bendiocarb, using Centers for Disease Control and Prevention (CDC) bottle bioassays. Unexposed, un-engorged female <i>Ae. aegypti</i> were tested individually for mixed-function oxidase (MFO), glutathione-<i>S</i>-transferase (GST) and α and β esterase activities. Finally, allele-specific PCR (AS-PCR) was used to detect possible <i>kdr</i> mutations (F1534C, S989P, and V1016G) in the voltage-gated sodium channel gene in insecticide-exposed <i>Ae. aegypti.</i> Most traps were oviposition positive; 93.2% and 97% of traps contained <i>Ae. aegypti</i> eggs in the 10^ème arrondissement of Cotonou and in Godomey-Togoudo, respectively. Insecticide bioassays detected resistance to permethrin and deltamethrin in both study sites and complete susceptibility to bendiocarb. By comparison to the insecticide-susceptible Rockefeller strain, field <i>Ae. aegypti</i> populations had significantly higher levels of GSTs and significantly lower levels of α and β esterases; there was no significant difference between levels of MFOs. AS-PCR genotyping revealed the possible presence of 3 <i>kdr</i> mutations (F1534C, S989P, and V1016G) at high frequencies; 80.9% (228/282) of the <i>Ae. aegypti</i> tested had at least 1 mutation, while the simultaneous presence of all 3 <i>kdr</i> mutations was identified in 13 resistant individuals. Study findings demonstrated phenotypic pyrethroid resistance, the over-expression of key detoxification enzymes, and the possible presence of several <i>kdr</i> mutations in <i>Ae. aegypti</i> populations, emphasizing the urgent need to implement vector control strategies targeting arbovirus vector species in Benin.