The evolution of pesticide resistance provides some of the most striking examples of darwinian evolution occurring over a human life span. Identification of resistance alleles opens an outstanding framework in which to study the evolution of adaptive mutations from the beginning of pesticide application, the evolution of interactions between alleles (dominance) or between loci (epistasis). Here we show that resistance alleles can also be used as markers to dissect population processes at a microevolutionary scale. We have focused on the antagonistic roles of selection and migration involved in the dynamics of local adaptation with reference to allelic frequencies at two resistance loci in the mosquito Culex pipiens. We find that their frequencies follow an annual cycle of large amplitude (25%), and we precisely unravel the seasonal variation of migration and selection underlying this cycle. Our results provide a firm basis on which to devise an insecticide treatment strategy that will better control the evolution of resistance genes and the growth of mosquito populations.