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Abstract Background Control of the mosquito vector Culex pipiens with insecticides is the main way to control arboviruses that the species can transmit such as West Nile virus (WNV) and Rift Valley fever virus (RVFV). However, its efficiency has been hampered by the emergence of insecticide resistance. Little is known about the insecticide-resistance status and underlying resistance mechanisms of field-collected populations of Cx. pipiens in Morocco. Methods Mosquito adults from Mohammadia city in Morocco were reared from immature stages. The level of their susceptibility to insecticides was assessed using standard WHO bioassay. The two forms of the Cx. pipiens complex and their hybrids were identified by a multiplex PCR. Identified mosquitoes were then tested for the presence of the G119S ace-1 and L1014F kdr mutations using PCR-RFLP and PCR assays, respectively. Results WHO bioassays indicated that Cx. pipiens was resistant to all tested insecticides: lambda-cyhalothrin (49% mortality), permethrin (63% mortality), DDT (16% mortality), malation (52% mortality) and bendiocarb (39% mortality). The frequency of the 119S allele was almost identical in the pipiens form and hybrids (0.11 and 0.15, respectively) whereas it remained low in the molestus form (0.03). No significant correlation was observed between the G119S allele and the resistance phenotype to two tested insecticides (malathion and bendiocarb). The frequency of the L1014F allele was identical in the pipiens form and hybrids (0.44) whereas it was low in the molestus form (0.36) but no significant difference was detected (χ2 = 1.46, df = 1, P = 0.225). The presence of the L1014F kdr mutation was significantly associated with resistance to three tested insecticides in pipiens form (P = 0.0019, P = 0.0023 and P = 0.023, respectively, to lambda-cyhalothrin, permethrin and DDT) whereas no significant correlation was observed between the L1014F kdr mutation and resistance phenotype in molestus form and hybrids to the three tested insecticides. Conclusion These findings showed that wild populations of Cx. pipiens have developed resistance against the main insecticide families with different modes of action: organochlorines (DDT), organophosphates (malathion), carbamates (bendiocarb), pyrethroids (lambda-cyhalothrin, permethrin). Therefore, urgent action should be taken to manage the resistance in this species to maintain the effectiveness of arbovirus control.