Information on gene flow among geographic and host populations of C. pomonella (L.) (Lepidoptera: Tortricidae) in South Africa is lacking, despite the importance of these measures for the success of control practices such as chemical control and sterile insect release, which are affected by the amount of gene flow among populations. Therefore, populations collected from nine geographically distant regions in South Africa from apples, pears, and stone fruit were compared using amplified fragment length polymorphism with five selective primer pairs. Results showed that although populations from different hosts were not genetically differentiated, significant evidence for population substructure was apparent between geographic populations. Over local scales, it was possible to distinguish between populations collected from orchards situated <1 km apart. These results suggest that although extensive gene flow occurs among populations from different hosts, gene flow among local geographic C. pomonella populations may be limited and is explained in terms of limited moth flight, the relative isolation of pome fruit production areas, and the absence of wild hosts.