Phylogenetic relationships among 16 genera of the subfamily Aphidiinae (Hymenoptera: Braconidae) were investigated using sequence data from three genes: the mitochondrial large ribosomal subunit (16S), 18S ribosomal DNA and mitochondrial ATPase 6. All sequences were downloaded from the GenBank database. A total of 2775 base pairs of aligned sequence were obtained per species from these three genes. The results support the existence of three-tribes: Ephedrini, Praini and Aphidiini, with the Ephedrini occupying the basal position; Aphidiini could be further subdivided into three subtribes: Monoctonina, Trioxina and Aphidiina. The genus Aphidius is a paraphyletic group. The taxonomic status of the subfamily Aphidiinae within the Braconidae is probably closer to the non-cyclostome than the cyclostome subfamilies.