Benin has embraced World Health Organization-recommended preventive strategies to control malaria. Its National Malaria Control Programme is implementing and/or coordinating various actions and conducting evaluation trials of mosquito control strategies. Mosquito control is based on the use of insecticide-treated nets and indoor residual spraying, but the efficacy of these strategies to control malaria vectors is endangered by insecticide resistance. Here, we present the results of a nationwide survey on the status of insecticide susceptibility and resistance in Anopheles gambiae s.l. (Diptera: Culicidae) carried out in Benin in 2006-2007 (i.e. before extensive vector control was undertaken). Overall, our study showed that the S molecular form of An. gambiae s.s. predominates and is widely distributed across the country, whereas the frequency of the M form shows a strong decline with increasing latitude. Susceptibility to DDT, permethrin, carbosulfan and chlorpyrifos-methyl was assessed; individual mosquitoes were identified for species and molecular forms, and genotyped for the kdr and ace-1 loci. Full susceptibility to chlorpyrifos-methyl was recorded and very few samples displayed resistance to carbosulfan. High resistance levels to permethrin were detected in most samples and almost all samples displayed resistance to DDT. The kdr-Leu-Phe mutation was present in all localities and in both molecular forms of An. gambiae s.s. Furthermore, the ace-1(R) mutation was predominant in the S form, but absent from the M form. By contrast, no target modification was observed in Anopheles arabiensis. Resistance in the An. gambiae S molecular form in this study seemed to be associated with agricultural practices. Our study showed important geographic variations which must be taken into account in the vector control strategies that will be applied in different regions of Benin. It also emphasizes the need to regularly monitor insecticide resistance across the country and to adapt measures to manage resistance. © 2010 The Authors. Medical and Veterinary Entomology © 2010 The Royal Entomological Society.