Codling moth (CM), Cydia pomonella L., is an important pest of apples worldwide. CM resistance to insecticides is a serious problem in apple production. For effective management and control, monitoring of resistant CM populations is absolutely necessary. Therefore, in this study, we investigated whether it is possible to find a reliable pattern of differences in CM populations related to the type of apple control method. The genetic results showed low estimated value of the pairwise fixation index, FST = 0.021, which indicates a lack of genetic differentiation and structuring between the genotyped populations. Different approaches were used to analyze the genetic structure of codling moth populations: Bayesian-based model of population structure (STRUCTURE), principal component analysis (PCA), and discriminant analysis of principal components (DAPC). STRUCTURE grouped the CM genotypes into two distinct clusters, and the results of PCA were consistent with this. The DAPC revealed three distinct groups. However, the results showed that population genetic differentiation between organic and integrated orchards was not significant. To confirm the genetic results, the forewing morphology of the same CM individuals was examined using geometric morphometric techniques based on the venation patterns of 18 landmarks. The geometric results showed higher sensitivity and separated three distinct groups. Geometric morphometrics was shown to be a more sensitive method to detect variability in genotypes due to pest control management. This study shows the possibility of using a novel method for a strategic integrated pest management (IPM) program for CM that is lacking in Europe.