To have an idea about the insecticide resistance profiles of Culex quinquefasciatus in one endemic district of Lymphatic Filariasis (LF) in Benin, susceptibility status of this mosquito in two urban areas (Founga and Zountori) and two rural areas (Nima and Bougou 2) to insecticides 0.75% permethrin, 0.05% deltamethrin, 4% DDT and 1% of bendiocarb was determined using the standard WHO susceptibility tests. Moreover, mutations in the acetylcholinesterase (ace-1) and knock down resistance (kdr) were screened from surviving mosquitoes using PCR methods. Results from the bioassays revealed that Cx. quinquefasciatus developed resistance to DDT (2% and 5% as average of mortality in urban and peri-urban areas, respectively), permethrin (14% and 22% in urban and peri-urban areas, respectively), deltamethrin (35% regardless of the areas of collection), but still susceptible to bendiocarb. Moreover, the kdr mutation was present in all populations of Cx. quinquefasciatus with frequency ranging from 0.89 to 0.9 and 0.86 to 0.87 in urban and rural areas, respectively. A low frequency (0.22 - 0.25 and 0.20 - 0.23 respectively in urban and rural areas) of ace-1 mutation was also found in the mosquitoes collected. These findings showed that Cx. quinquefasciatus populations of Djougou have developed resistance to organochlorine, pyrethroids with a high level of kdr mutation. The low level of ace-1 mutation suggested that insecticides belonging to carbamate and organophosphate families could be used to control Cx. quinquefasciatus in this district, however, regular surveillance needs to be conducted on the susceptibility of this mosquito to the insecticides of these families.