The oriental fruit fly, Bactrocera dorsalis, is highly polyphagous pest that damages over 400 plant species, including commercially grown crops and fruits. It was first described in Taiwan and has since invaded Japan and China. In 2021, B. dorsalis was reported on Jeju Island in the Republic of Korea (ROK). To investigate its origin and understand its colonization pathway in ROK, the genetic characteristics were analyzed by using mitochondrial genes. The study analyzed the haplotypes and genetic differences among populations oriental fruit flies collected from Southeast Aisa, including Thailand, Taiwan, and Vietnam. The mitochondrial genes cytochrome oxidase subunit I (COI) and cytochrome B (CytB) were used for the analysis. The results showed that B. dorsalis had high levels of haplotype diversity among species. No major haplotype was found among populations. The present study enhances our understanding of the haplotype diversity of B. dorsalis in neighboring countries of ROK. This will expand our knowledge of the source of origin and invasive pathway for B. dorsalis.