The objectives of this study are to examine the genetic variation in oriental fruit flies (Diptera: Tephritidae) and to use it as a barcode for the origin elucidation, in preparation for the their incursions into Korea. About 1,600 specimens of B. dorsalis sp. complex and B. correcta were collected from 10 countries, the Indochina peninsula, the Philippines, Taiwan and South China. A total of 182 cytochrome c oxidase (COI) sequences were obtained and aligned from these regional specimens. Three sequences from the Genebank reference were also included. Six hundreds base pair fragments were aligned and trimmed and used for a barcode. The phylogenetic tree was generated using the neighbor-joining method with 1,000 bootstrap replicates. There were two distinct groups in the phylogenetic tree, Bactrocera dorsalis sp. complex and B. correcta. Three specimen, intercepted in the hand-carried mango at the airport inspection and collected in the confiscated mango, smuggled from Vietnam were included for a test. The DNA from the airport were 100% identical to that of one of various Vietnam specimens, and that from the confiscated mango was mostly similar to those of Vietnam, suggesting the usefulness of the barcode for the origin elucidation tool of oriental fruit fly.