Parasitoid wasps offer an ample opportunity to study host-parasite coevolution. Thorough description of their inter- and intra-specific variation in host range and taxonomy is a crucial step toward understanding causes and consequences of coevolution. Ganaspis is one of the major genera of Drosophila parasitoids. Ganaspis xanthopoda, the most abundant species of this genus in East Asia, has been suggested to contain at least two diverged clades: one attacking D. suzukii, and the other attacking mainly D. lutescens in Japan. However, the level of divergence and diversity within this species throughout the East Asian region are unknown. In this study, we examined molecular phylogeney of individuals that have been identified as G. xanthopoda by morphological characteristics. We showed that this species is found from a much broader range of geographic region and climate of East Asia than related groups of parasitoids, and its phylogenetic status is clearly distinct from undescribed congeneric in the region. We discuss further implications based on experiments on reproductive isolation and adaptation to low temperature in laboratory strains of G. xanthopoda from Japan and Taiwan.