Wolbachia symbionts are responsible for various alterations in host reproduction. The effects of the host genome on endosymbiont levels have often been suggested, but rarely described. Here, we show that Wolbachia density is strongly modified by the presence of insecticide-resistant genes in the common house mosquito, Culex pipiens. The Wolbachia density was estimated using a real-time quantitative PCR assay. Strains harbouring different genes conferring resistance were more infected than a susceptible strain with the same genetic background. We show that this interaction also operates in natural populations. We propose that mosquitoes may control Wolbachia density less efficiently when they carry an insecticide-resistant gene, i.e. when they suffer from a physiological resistance cost.