The olive fruit fly (Bactrocera oleae Gmelin) is the most important olive pest in the north‐eastern Adriatic coast region. Despite the importance of olive production in the region, and the significance of the olive fruit fly, no information with respect to genetic diversity, population structure or dispersion patterns of this pest is available. The aims of this study were to investigate the genetic structure of the olive fly population in the Slovenian Istria region using microsatellite markers to determine olive fruit fly migration between locations and to establish an appropriate and effective strategy for controlling the pest population. Analysis was performed on a sample of 117 flies, collected from attacked olive fruits at three different locations. Olive fruit flies were genotyped using eight microsatellite loci. Sixty‐six alleles were identified over all microsatellite loci with an average of 8.25 alleles per locus. The population structure was determined with methods based on Bayesian principles using the BAPS 6.0 and STRUCTURE 2.3 programs. Genetic analysis confirmed unlimited migration and random mating between individuals of different microlocations, which suggests time‐coordinated first treatment in the region would be the best solution.