We studied the prevalence of the exotic parasitoid fly, Nealsomyia rufella, which attacks the native giant bagworm, Eumeta variegata in Japan. Although invasion of N. rufella in the late 90s has been reported to rapidly decrease the populations of E. variegata, little is known about the subsequent population dynamics of E. variegata and the parasitism by N. rufella. Sampling survey of E. variegata in the central and western part of Japan revealed the persistent distributions of E. variegata populations in spite of high percentage of N. rufella parasitism at almost all sampling sites throughout Japan. In addition, the phylogenetic study using DNA markers found two genotypes of N. rufella which are identical to those found at the continental China. While this result is consistent with the hypothesis that the invaded N. rufella populations in Japan originated from China, further analysis is needed to infer the route of N. rufella invasion.