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Simple Summary: The more the global agricultural product trade becomes active every year, the more foreign pests' invasion probability increases. Accordingly, many notorious invasive pests are spreading worldwide, and the nations should try to block their introduction through quarantine systems. As an important quarantine pest, the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), is one of the most destructive pest insects for fruit crops in tropical and subtropical areas. This species is a highly invasive and economically important pest with a broad host range. Here, we collected 40 geographically or temporally different collections from 12 Asian countries, including four from the Korean border quarantine detection, and performed haplotype analysis and population genetics analysis. To infer the introduction sources of the oriental fruit fly, Bactrocera dorsalis, we used a mitochondrial marker to reconstruct the haplotype network and 15 microsatellite loci to reveal genetic structure and relationships between the geographically or temporally different collections from Asia. We performed Approximate Bayesian computations to infer a global origin and a source of the quarantine collections found in Korea. As a result, the 40 populations were divided into three groups, of which genetic similarity is not related to the geographic vicinity. Korean samples had a similar genetic structure to Taiwan and Thailand ones. Our results suggest that the place of origin of the B. dorsalis specimens found in Korea's border quarantine is likely to be Taiwan or Thailand. As the global origin of B. dorsalis, we estimated that Taiwan and Thailand were most likely the global origins of Southeast Asian populations by testing hypothetical scenarios by the approximate Bayesian computation analyses. Our results will allow easier identification of the source region of the forthcoming invasion of quarantined B. dorsalis specimens. [ABSTRACT FROM AUTHOR]