The genus Aphidius is the most commercially available species in greenhouse control, especially for aphids. Although twelve species were recorded in Korea, we collected 7 species including 2 unrecorded and 1 unidentified species. We aligned 16 sequences, except for duplicates, from 31 individuals of 14 species including GenBank sequences, and made phylogenetic tree based on Neighbor-Joining method. Surprisingly, 3 species were clustered into a clade and some species was not monophyletic. In this study, we reconstructed phylogenetic tree of Korean Aphidius species using COI marker, and compared them with GenBank sequences. In addition, we try to experiment a new marker and check its ability of discrimination.