Three tortricid pests, Grapholta dimorpha (Komai), G. molesta (Busck), and Carposina sasakii (Matsumura) are known as internal apple feeders in Korea. For identify young larvae which occurring serious damage in fruits, the molecular maker was developed from their mitochondrial DNA (mtDNA) sequences. To develop of PCR-RFLP marker, ND4 locus was digested with Swa Ⅰ. ND4-Swa Ⅰ digests showed two bands (396, 292 bp), one band (700 bp), and three bands (408, 178, and 103 bp) of G. dimorpha, G. molesta, and C. sasakii, respectively. Species-specific diagnostic PCR primers were developed in the ND4 locus and gave species-specific PCR products. Finally, these markers were applied to diagnose larvae infesting apples and showed species-specific fruit damage patterns, in which most feeders of G. dimorpha, G. molesta, and C. sasakii showed major feedings in apex, surface, and core of apple fruits, respectively.