The oriental fruit moth (Grapholita molesta) and the plum fruit moth (G. dimorpha) are internal feeders of stone and pome fruits and highly similar in morphological characters and feeding behaviors. These two species share their two main sex pheromone components, Z8-dodecenyl acetate(Z8-12Ac) and E8-dodecenyl acetate(E8-12Ac) although pheromone compositions are different. But, two males of these species were cross-attracted to G. molesta and G. dimorpha pheromone trap, respectively. Their host plants are also very similar in Rosaceae including apples, plums, paches, etc. These sympatric and similar pheromone ratios and biological characters suggest their recent speciation divergence. To determine genetic origin of this speciation, were analysed transcriptomes associated in sex pheromone biosynthesis in these sibling species. Total RNAs were collected from pheromone glands and read by a short read deep sequencing technology using an lllumina HiSeq2000. Almost 3-4 Gb reads were de novo assembled and resulted in 76,361 contigs of G. dimorpha and 104,463 contigs of G. molesta. More than 70% of these contigs were annotated and classified by a typical GO analysis. Transcriptomes related with sex pheromone biosynthesis were selected and grouped into fatty acid synthase, fatty acid oxidation, desaturase, reductase, and isomerase. These analyses identified sex pheromone biosynthesis machineries, which showed significant differential expressions between two sibling species. Field monitoring assays indicated the minor components (Z8-12OH) resulted from fatty acid reductase were crucial in isolating two sibling species.