The olive fly is the most dangerous pest of the olive fruit. Infestation with the olive fly reduces the quality and yield of the olives and thus also the quality of the olive oil. In the Republic of Croatia, domesticated olive varieties are grown alongside native olives, which can be infested by this pest to varying degrees. The aim of the work was to determine the morphological variability of olive fly populations using the method of geometric morphometrics on the wings of pests collected on native and domesticated olive varieties in coastal cultivation areas in the Republic of Croatia. In olive groves in Istria (Vodnjan) and northern Dalmatia (Benkovac), the fruits of different olive varieties (indigenous – 'Oblica' and 'Istarska bjelica' - and domesticated – 'Ascolana tenera', 'Frantoio', 'Leccino' and 'Pendolino') were collected. The olive fly samples were taken from collected olive fruits. A total of 664 olive fly individuals were collected and their wings were removed and slide-mounted according to the standard procedure. The wings were then photographed, and 20 landmarks at the intersections and ends of the veins were digitized on each image to perform geometric morphometric analyzes. When standard geometric morphometric analyzes were applied to the wings of the olive fly, significant differences in the shape of the wings were found between the females and males of the populations studied, clearly demonstrating the sexual dimorphism of the species. In addition, significant differences in the shape of the wings of the olive fly were found between different olive varieties. The results of this study confirm that the analysis of the geometric morphometry of the wings is suitable to identify specific phenotypes of a pest that successfully reproduces and spreads in different olive cultivars.