The results of the PCR analysis of two codling moth populations using RAPD and SSR markers are presented. The molecular genetic structure of investigated pest populations is described and its variability under influence of insecticides, varying climatic conditions during 2008 to 2011 and geographic location is studied. The intra-population genetic diversity by two microsatellite loci was estimated in pests from the gardens with different insecticide press. Genetic diversity of codling moth populations was shown to depend mainly on genetic features of the populations, bur not on the insecticide load or weather conditions.