Microsatellites were used to investigate the genetic structure and gene flow of three codling moth (Cydia pomonella Linnaeus; CM) populations in Croatia. Two populations were subjected to chemical control treatments for the last 15 years, and one population was not subjected to any chemical control treatment. During the assessment of genetic differentiation, only the males caught in pheromone traps were used. Ten variable microsatellites revealed strong allelic variation. The number of alleles (Na) varied from 2 (at loci Cyd 15 and Cyd 14) to 13 (at locus Cp 2.39), with an average value of 7.20 alleles per locus. The observed (HO) and expected heterozygosity (HE) per locus ranged from 0.5 to 0.76 and 0.10 to 0.84, respectively. The measures of pair-wise population genetic structure (FST = 0.02 - 0.04) were low and not significant in all of the comparisons (after correction for multiple comparisons). Additionally, an analysis of molecular variance (AMOVA) performed on the three populations, which were grouped geographically according to the type of management or according to the variation across generations (second or third generation individuals), revealed no significant variance in the genetic structure. However, the genetic variation was significantly partitioned within individuals (70-96%). Additionally, the tests for isolation by distance were not significant, suggesting a need to analyse the specifics of human-mediated CM transport over short and long distances within the Croatian apple-growing regions as a possible cause of gene flow. This study supports the hypothesis of genetic exchange in codling moths between orchards at moderate to potentially high levels.