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Background  Insecticide resistance in  Anopheles  mosquitoes is threatening the success of malaria control programmes. In order to implement suitable insecticide resistance management strategies, it is necessary to understand the underlying mechanisms involved. To achieve this, the molecular basis of permethrin and DDT resistance in the principal malaria vector,  Anopheles funestus  from inland Benin (Kpome), was investigated.    Results  Here, using a microarray-based genome-wide transcription and qRT-PCR analysis, we showed that metabolic resistance mechanisms through over-expression of cytochrome P450 and glutathione S-transferase genes (GSTs) are a major contributor to DDT and permethrin resistance in  Anopheles funestus  from Kpome. The  GSTe2  gene was the most upregulated detoxification gene in both DDT- [fold-change (FC: 16.0)] and permethrin-resistant (FC: 18.1) mosquitoes suggesting that upregulation of this gene could contribute to DDT resistance and cross-resistance to permethrin.  CYP6P9a  and  CYP6P9b  genes that have been previously associated with pyrethroid resistance were also significantly overexpressed with FC 5.4 and 4.8, respectively, in a permethrin resistant population. Noticeably, the GSTs,  GSTd1-5  and  GSTd3 , were more upregulated in DDT-resistant than in permethrin-resistant  Anopheles funestus  suggesting these genes are more implicated in DDT resistance. The absence of the L1014F or L1014S  kdr  mutations in the voltage-gated sodium channel gene coupled with the lack of directional selection at the gene further supported that knockdown resistance plays little role in this resistance.    Conclusions  The major role played by metabolic resistance to pyrethroids in this  An. funestus  population in Benin suggests that using novel control tools combining the P450 synergist piperonyl butoxide (PBO), such as PBO-based bednets, could help manage the growing pyrethroid resistance in this malaria vector in Benin.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-3115-y) contains supplementary material, which is available to authorized users.

Molecular basis of permethrin and DDT resistance in an Anopheles funestus population from Benin