Genetic differentiation in ecological traits plays an important role in the reproductive isolation of phytophagous insects. The present study aims to elucidate the genetic changes involved during the process of host shifts, by combining analyses for (1) host adaptations, (2) pre-and postmating isolation, and (3) phylogeney among populations, using a leaf-mining moth, Acrocercops transecta. This species is associated with Juglans ailanthifolia and Lyonia ovalifolia. Transplantation of the larvae demonstrated that the Juglans-associated population completely failed to survive on Lyonia, whereas the Lyonia-associated population survived on Juglans as well as on Lyonia. Females of respective host-associated populations oviposited on their natal host plant only. An mtDNAbased phylogeny clearly separated the Lyonia-associated population from the Juglandaceae-associated population, and indicated that the Lyonia-associated population once evolved from the Juglandaceae-associated population. These results indicate that the processes of host shifting from juglandaceous species to Lyonia involved genetic changes both in larval ability to use host plants and in host preference of females. The derived Lyonia-associated population has retained the potential to assimilate the ancestral host, Juglandaceae. Mating between the two host-associated populations was successful for both directions of crossing, and there were no significant differences in egg hatchability between hybrids and control crosses. No adults emerged when the F1 hybrid larvae were maintained on Lyonia; however, on Juglans the F1 hybrid larvae grew to adulthood as well as in the control, suggesting a lack of genomic incompatibilities between the two host-associated populations. In conclusion, the results showed that the two host-associated populations are host races that are partially reproductively isolated, and that the differences in performance and preference function as strong barriers against gene flow between the host races.