The codling moth, Cydia pomonella, is renowned for developing resistance to insecticides and causing significant economic damage to pome fruits worldwide. In spite of its economic importance, little is known about the patterns of movement of this pest and the effects of insecticide treatment on the population genetic structure. Here, we investigated the genetic structure of the pest in 27 orchards from France, Italy, Armenia and Chile at seven microsatellite loci and two resistance markers [biochemical activity of cytochrome P450 oxidases and proportion of knockdown resistance (kdr) alleles in the sodium channel gene]. According to the microsatellite loci, we detected isolation by distance at the supranational scale but found no evidence of geographical structure among the 24 French orchards, which were mainly structured by the intensity of the insecticide treatments. Similarly, the highest levels of metabolic resistance associated with activity of the cytochrome P450 oxidases were detected in the most treated orchards. The kdr alleles were observed in southern France and Armenia where the pyrethroid insecticides were or have been intensively sprayed. The intensity of the insecticide treatments marginally affected the allelic richness in each orchard, but not the level of inbreeding. These results suggest important and high-distance gene flow among the codling moth populations, which were mainly structured according to the history of insecticide applications. Differences in mutation-migration-drift equilibrium among treated and untreated orchards also suggest that insecticide applications are the main force regulating the local dynamics of codling moth populations.