The Mediterranean fruit fly or medfly, Ceratitis capitata (Wiedemann, 1824) is one of the most economically important fruit flies globally. Geometric morphometric methods based on principal component analyses, multivariate regressions and two blocks partial least squares analyses were used in this study to estimate patterns of sexual shape dimorphism and the influence of agroecological factors (weather conditions, soil properties) in two different populations on C. capitata in Croatia. Results shown significant differences in mean shape between C. capitata sexes, nevertheless, females did not modify they wing morphology between populations, in contrast to males where the wing shape differ between island and continent populations. Wing size and shape showed particularly differences between agroecological systems suggesting metapopulation structure of C. capitata which is currently favouring sex-specific plasticity. These results show that geometric morphometric procedures can be used to provide key insight into the biological adaptation of medfly in newly invaded habitats, a significant process that ensures invasion success.