Amplified fragment length polymorphism (AFLP) fingerprints were used to characterize the population genetic structure and gene flow of the oriental fruit moth, Grapholita molesta (Busck) (Lepidoptera: Tortricidae), for the first time in the major stone-fruit growing regions in South Africa. Populations were collected from six different regions and compared with each other. Furthermore, intraregion gene flow was determined by sampling more extensively from farms and orchards within two of these six regions. Five selective AFLP primer pairs generated 250 fragments. Phylogeny analysis clustered populations from the six regions into two main groups, although those situated close together geographically were not necessarily closely related genetically. Over local scales, populations collected from closely situated orchards (<1 km) could be distinguished. It seems that G. molesta was introduced at least twice into South Africa and that although moth dispersal over local scales may be limited, leading to the formation of localized populations, factors such as movement of fruit, bins, and nursery material among areas also may have helped extend the range of this insect in South Africa. These results provide important information on the population genetics of G. molesta for the design and implementation of sustainable pest management strategies, such as the management of insecticide resistance, which is influenced by insect dispersal.