Two Grapholita congeners, G. dimorpha and G. molesta, are internal fruit feeders and their young larvae cause serious damages to pome and stone fruits in Korea. They share similar morphological and biological characters not to be easily discriminated. We needed to develop molecular markers using diagnostic primers and PCR-RFLP with specific sequences in ND4 region. Two species have similar sex pheromone components (Z8-12:Ac and E8-12:Ac) although their composition ratios are different. In fields, G. molesta males were more captured in lures with higher Z8 component ratio than G. dimorpha males. Addition of Z8-12OH, minor sex pheromone component prevented G. dimorpha from capturing G. molesta males. In electroantennogram (EAG) bioassay, these two species males showed significant electric responses in their own sex pheromone ratios. An addition of Z8-12:OH to the major sex pheromone components significantly suppressed the EAG response of G. dimorpha, while it did not change that of G. molesta. A deep sequencing analysis of transcripts of both species pheromone glands identified sex pheromone biosynthesis genes including fatty acid synthase, desaturases, fatty acyl reductase (FAR), and aldehyde reductase. The presence of delta 10 desaturase in both species suggests that a double bond at C8 position in dodecenyl acetate is produced by desaturation at C10 position of tetradecenyl fatty acid and subsequent β-oxidation, which is then reduced at carboxylic acid by FAR to be acetylated by acetyl transferase. High sequence variation of FAR genes of G. molesta and G. dimorpha suggests their stereoisomer substrate preference, which may exert a driving force for this speciation with delta 10 desaturase.