Analysis of population genetic structure is a key aspect to understand insect pest population dynamics in agricultural scenarios. Here the role of geography, hosts and time on the population genetic structure of codling moth Cydia pomonella (Linnaeus) (Lep., Tortricidae) populations is described. Temporal variation was examined in two French orchards among each of three adult flights during two successive years. Analyses were conducted using two insecticide resistance markers (variation at the sodium channel gene and enzymatic activity of cytochrome P450 oxidases) and three microsatellite loci. Levels of genetic variation among temporal populations were not significant based on variation in the sodium channel gene and microsatellite loci. However, P450 oxidase activity differed significantly during both flights and years, decreasing during the three flights of the first year and increasing during the second. These results suggest that phytosanitary measures are among the factors shaping the genetic structure of C. pomonella populations over temporal and geographical scales. We discuss the relative importance of natural and passive dispersal related to anthropogenic activities affecting C. pomonella population genetics and highlight population genetic research needs in order to design more efficient pest management practices.