Information on Culex mosquitoes (vectors of filarial worm and viral encephalitis) from northern Nigeria is scanty, hindering evidence-based control. Here, two Culex populations (Kano and Kaduna) were characterized. Culex quinquefasciatus and Culex pipiens were found breeding in sympatry, with some hybrid individuals identified. Larval bioassays revealed high temephos resistance (LC50s = 1.34 mg/mL and 3.01 mg/mL for Kano and Kaduna, respectively). Larvae were more sensitive to α-cypermethrin (LC50s = 0.026 mg/mL and 0.067 mg/mL for Kano and Kaduna). WHO adult tube bioassays revealed high pyrethroid and DDT resistance, with mortalities of 44.01% ± 6.79%, 35.83% ± 12.58%, 29.69% ± 9.97% and 52.47% ± 4.34% for permethrin, deltamethrin, α-cypermethrin and DDT, respectively. Highest resistance was observed with bendiocarb (mortality = 13.58% ± 3.98%). High resistance was obtained with fenitrothion and malathion (mortalities = 21% ± 4.76% and 56.47% ± 8.67%, respectively), while a full susceptibility was observed with pirimiphos-methyl. Pre-exposure to piperonylbutoxide (PBO) significantly recovered α-cypermethrin susceptibility (mortality = 82% ± 5.16%, χ2 = 50.99, p kdr genotype and resistance phenotype. Sequencing of fragments of the acetylcholinesterase-1 gene detected no G119S mutation, in malathion-alive and malathion-dead females. These suggest a preeminent role of metabolic resistance in these Culex populations.