West Nile (WN) virus has been detected in Guadeloupe since 2002. Even if no WN human cases have been detected so far, mosquitoes from Culex genus especially Culex quinquefasciatus are recognized as potential WN vectors in Guadeloupe. To evaluate the impact of local vector control activities on this mosquito species we assessed the resistance levels of Cx. quinquefasciatus populations from three different sites from Guadeloupe (Abymes, Saint François and Gourbeyre) to malathion, temephos and deltamethrin. In addition, the frequencies of the L1014F kdr and the G119S ace-1 mutations were established in Cx. quinquefasciatus populations, as well as the constitutive expressions of five cytochrome P450 genes. Mosquito populations tested displayed high resistance to deltamethrin, moderate resistance to malathion (Abymes, Gourbeyre) and low resistance to temephos (Abymes et Gourbeyre). Molecular analyses revealed high frequencies of both L1014F kdr and G119S ace-1 mutations in Cx. quinquefasciatus populations, as well as overexpression of cytochrome P450 genes CYP9J45, CYP9J40 and CYP6AA7. Finally, deltamethrin resistance and knock-down rates were strongly correlated with the frequency of the resistant kdr and ace-1 alleles, as well as with CYP9J40 overexpression. These results should be taken into account to refine the current vector control strategies to prevent the appearance of Cx. quinquefasciatus-borne diseases in Guadeloupe.