Oriental fruit moth, Grapholita molesta, is a serious pest on apples. To control this pest in an environmentally friendly method, mating disruption strategy using sex pheromone has been developed. Area-wide application of mating disruption has been needed to be effective, with little understanding on how much size of apple cultivating area should be treated in one time application of the mating disruption technique. On this matter, we needed to determine a minimal mating active zone of G. molesta that should be applied with mating disrupters to be effective. Molecular markers to discriminate a specific population should be developed to trace population migration for reproductive behaviors. Here we developed two effective molecular markers using random amplified polymorphic DNA (RAPD) technique. Different field populations of G. molesta, based on locations and seasons, were analyzed with these markers. In a specific location, G. molesta populations varied in genetic composition with different seasons. Different local populations showed differential variation according to their relative distances among apple orchards. In overall, genetic variation among different populations became lessen with progression of seasons.