In the 21st century, the risk of the exotic pest being invaded is increasing due to the rise of trading activities. Oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae), has been considered to very destructive invader as it is highly intrusive and has a wide host range. In this study, 2,299 samples were collected from 88 locations in 12 countries by quarantine and investigation. Among them, 608 individuals (including B. correcta) were used for COI DNA barcoding analysis based on Neighbor Joining method with P-distance model. Population genetics analysis was conducted for 510 individuals selected from 47 locations of 12 Southeast Asian countries using 15 microsatellite loci. The barcoding analysis resulted in that any clade was not clustered according to a geographical isolation but indicated geographically mixed populations. Population genetics analysis showed shared genetic structure between neighboring countries across borders. Genetic structure of most Korean quarantine groups was more similar to that of Taiwan, China and Thailand in the order of appearance than other countries.