The true fruit flies (Diptera: Tephritidae) are major agricultural pests worldwide. In Korea, imported crops are carefully scrutinized to prevent infestation by exotic tephritids and rapid species idnetification is required to make quarantine decisions. At quarantine checkpoints, tephritids are most commonly intercepted at the larval stage, however larvae have few diagnostic morphological features. Here we describe a molecular genetic method using restriction enzyme digestions of PCR products from the mitochondrial gene, cytochrome oxidase I(COI). This technique provides a simple diagnostic marker for Korean fruit flies in the genus Bacterocera(B. depressa, pumpkin fruit fly; and B. scutellata, pumpkin flower fruit fly) and wide spread fruit flies (B. dorsalis, oriental fruit fly; and Ceratitis capitata, medfly). The restriction enzymes ApaI, NheI and SacI were used to digest the 815 bp PCR product into fragments that uniquely diagnose each species. The simplicity and relatively low cost of this molecular approach will facilitate rapid quarantine decisions concerning exotic fruit flies.