Rapid identification of pest species found under quarantine is an important factor in preventing an economic loss of agricultural commodities. In this study, we analyzed RNA-Seq of the larvae of C. sasakii, G. molesta and G. dimorpha, which are serious pests in several fruits in Korea and are difficult to discriminate by species in their larval stage because of lack of a morphological character. To select immunological diagnostic markers, discriminating the larvae of C. sasakii from the G. molesta and G. dimorpha, RNA-Seq was performed for the larvae of the three insects. The 454 pyrosequencing generated 3,058-4,686 contigs for each three pest species, which assembled into 2,584-3,970 isotigs with average lengths of 829-1,244 bp. Functional annotation of the sequencing results generated 774 orthologs for the three pest species, and 12 isotigs were finally registered as candidate markers for species discrimination through bioinformatical screening, literature search, and gene expression study. The selected candidates include serine proteases, serpins, 27 kDa glycoprotein and storage protein with a constitutive gene expression in their larvae, pupae and adult stage.