The oriental fruit moth (Grapholita molesta) and the plum fruit moth (G. dimorpha) are internal feeders of apples. Their sympatric and similar sex pheromone compositions suggest their recent divergence in speciation. This study aims to determine genetic factors in this speciation by comparing transcriptomes associated in sex pheromone biosynthesis in these sibling species. Total RNAs were collected two female abodominal tips and read by a short read deep sequencing technology using an lllumina HiSeq. 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. These analyses identified sex pheromone biosynthesis machineries