Delimiting species remains a major challenge in taxonomy, particularly in groups with a minute size and high morphological similarity, such as the hyperparasitoid wasps of the subfamily Charipinae (Hymenoptera: Cynipoidea: Figitidae). Accurately selecting morphological characteristics is very important for distinguishing species, yet many traditional diagnostic traits may be unreliable due to high intraspecific variability. In this study, we applied an integrative taxonomy approach to assess species boundaries in ten species of the Alloxysta (A. brevis, A. castanea, A. obscurata, A pilipennis, A. ramulifera and A. victrix) and Phaenoglyphis (P. heterocera, P. longicornis, P. villosa and P. xanthochroa) genera. We critically evaluated morphological characteristics traditionally used in Charipinae taxonomy and tested their reliability by comparing them with molecular data from three genetic markers: mitochondrial COI, nuclear ITS2, and ribosomal 16S. Phylogenetic analyses confirmed that charipine species delineation based on morphological features is usually correct. Our results underscore the importance of integrating molecular and morphological evidence to refine species boundaries and improve the classification of hyperparasitoid wasps. By establishing a more robust framework for species identification, this study not only enhances our understanding of biodiversity within the Charipinae taxonomy but also provides essential insights for future ecological and evolutionary research involving these intricate parasitic relationships.