[Objectives]  To establish effective management measures for the striped fruit fly, Zeugodacus scutellatus (Hendel) (Diptera: Tephritida), an important quarantine species in China, and prevent further expansion of its range by identifying its mode of expansion and historical expansion routes. [Methods]  The population genetic structure and contemporary gene flow of the striped fruit fly were assessed based on variation in the mtDNA cox1 and cox2 sequences. [Results]  Haplotypesdiversity (h), Nucleotide diversity (π), F_st and Gene flow (N_m) were higher in western populations than in eastern ones. These parameters are also higher in the Japanese population than in Chinese populations. Evaluation of haplotype phylogenetic structure indicates that all haplotypes from Japan clustered at the base of the phylogenetic tree, indicating that these haplotypes are more ancient than those found in China. The results of a Mantel Test indicate that Z. scutellatus populations have suffered bouts of high-speed expansion in China, and that geographical barriers have been no obvious impediment to their spread. [Conclusion]  Our results indicate that Chinese populations of Z. scutellatus probably originated from Japan, and that Shanghai and Chongqing were the first two places in China to be colonized. Z. scutellatus probably arrived in two waves, one establishing in Shanghai simultaneously with imports from Japan, then, facilitated by trade along the Yangtze River, quickly colonizing the Yangtze Delta and inland regions. Another wave arrived in Chongqing, the commercial center of western China, including Yunnan, Sichuan, Gansu, Guizhou and Shaanxi provinces. Expansion north and south from Chongqing was also facilitated by the movement of produce and goods.