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Abstract Background In the Republic of Congo, with two massive outbreaks of chikungunya observed this decade, little is known about the insecticide resistance profile of the two major arbovirus vectors Aedes aegypti and Aedes albopictus. Here, we established the resistance profile of both species to insecticides and explored the resistance mechanisms to help Congo to better prepare for future outbreaks. Methods Immature stages of Ae. aegypti and Ae. albopictus were sampled in May 2017 in eight cities of the Republic of the Congo and reared to adult stage. Larval and adult bioassays, and synergist (piperonyl butoxide [PBO]) assays were carried out according to WHO guidelines. F1534C mutation was genotyped in field collected adults in both species and the polymorphism of the sodium channel gene assessed in Ae. aegypti. Results All tested populations were susceptible to temephos after larval bioassays. A high resistance level was observed to 4% DDT in both species countrywide (21.9–88.3% mortality). All but one population (Ae. aegypti from Ngo) exhibited resistance to type I pyrethroid, permethrin, but showed a full susceptibility to type II pyrethroid (deltamethrin) in almost all locations. Resistance was also reported to 1% propoxur in Ae. aegypti likewise in two Ae. albopictus populations (Owando and Ouesso), and the remaining were fully susceptible. All populations of both species were fully susceptible to 1% fenitrothion. A full recovery of susceptibility was observed in Ae. aegypti and Ae. albopictus when pre-exposed to PBO and then to propoxur and permethrin respectively. The F1534C kdr mutation was not detected in either species. The high genetic variability of the portion of sodium channel spanning the F1534C in Ae. aegypti further supported that knockdown resistance probably play no role in the permethrin resistance. Conclusions Our study showed that both Aedes species were susceptible to organophosphates (temephos and fenitrothion), while for other insecticide classes tested the profile of resistance vary according to the population origin. These findings could help to implement better and efficient strategies to control these species in the Congo in the advent of future arbovirus outbreaks.