[Objectives]  To ascertain whether geometric morphometrics is a reliable method for identifying species of the genus Bactrocera, which are challenging to identify due to their similar morphology. Accurate identification is important because the great majority of species in this genus are economically important quarantine pests. [Methods]  Geometric morphometrics was used to evaluate wing size and shape variation among three important species of the genus Bactrocera’s subgenus Zeugodacus. Ninteen landmarks were measured on the right wings of 180 male specimens from these 3 species and used to generate geometric morphometric size and shape data. The wing size and shape information were analyzed based on Centroid size, Procrustes superimposition, Principal component analysis (PCA), Multivariate analysis of variance (MANOVA) and Thin plate spline analysis (TPS). [Results]  A one-way ANOVA of centroid size indicated that there were significant differences (F=141，df=179，P<0.001) in wing size among the three species: Bactrocera (Zeugodacus) scutellata (Hendel) had the biggest wing centroid size, B. (Z.) tau (Walker) the next largest, and B. (Z.) cucurbitae (Coquillellett) the smallest. PCA and MANOVA showed that there were significant differences in wing shape among the three species, and TPS showed that wing differences among the three species were mainly in the distal 5^th radial cell and distal 2^nd medial cell. [Conclusion]  Fruit flies of the genus Bactrocera can be reliably identified by geometric morphometrics, a new tool for identifying species of this genus.