Two fruit moths of the oriental fruit moth, Grapholita molesta (Busck), and the peach fruit moth, Carposina sasakii (Matsumura), infest apples in Korea by internally feeding behavior. C. sasakii is a quarantine insect pest from some other countries importing Korean apples. G. molesta is not a quarantine insect pest, but can be incorrectly identified as C. sasakii especially when it is found inside apple fruits at its larval stages because it is not easy to identify the two species by morphological characters alone. This incomplete identification results in massive economical loss by fruits needlessly destroyed or turned away at border inspection stations of the importing nations. This difficulty can be overcome by molecular DNA markers. Several polymorphic regions of mitochondrial DNA of both species were sequenced and used for developing specific restriction sites and polymerase chain reaction (PCR) primers. Based on these sequences, three diagnostic PCR-restriction fragment length polymorphism (RFLP) sites were detected and validated for their practical uses. Also, species-specific PCR primers were devised to develop diagnostic PCR method for identifying the internal feeders.