Previous studies indicated that Matsumuraeses phaseoli and M. falcana (Lepidoptera: Tortricidae) are separate species since a few differences were observed in genitalia morphology and female sex pheromone composition. A clear difference was detected in the DNA sequences of cytochrome oxidase I of the two species separately collected in different plants and regions. A hybridization test also showed that a post-zygotic reproductive isolation occurred between the species. In field monitoring, however, both species have been caught simultaneously and together in the separate sex pheromone traps installed for the two species around neighboring soybean and red bean fields. Molecular marker-assisted identification with several adults sampled from the trapped insects showed that only ca. 40% of M. phaseoli adults identified as the species by genitalia morphology was the M. phaseoli, while ca. 97% of M. falcana adults identified as the species was the M. falcana. The result indicated that the observation of genitalia did not make a decisive criterion for classification of the insects. Conclusively, it suggested that the sex pheromones of the two species should be studied more precisely although there is a possibility that the two species are hybridized in fields as in laboratory, and speciation is under process.