Opiinae (Hymenoptera: Braconidae) is an important parasitoid of fruit flies (Diptera: Tephritidae). Accurate identification is needed for them to be effectively used as biological control agents. This study demonstrates the use of molecular phylogenetic analyses to reconfirm the species of Opiinae reared from tephritids infesting star fruit species. A total of 14 specimens were isolated and a 401 bp of mitochondrial 16S rRNA gene was amplified and sequenced from each of them. Three individual tephritids hosts (Bactrocera papayae) were also identified based on the mitochondrial ND1 gene. Maximum Parsimony (MP) tree was constructed using PAUP 4.0b10. Three species of Opiinae were successfully identified based on the mitochondrial 16S rRNA gene, namely Diachasmimorpha longicaudata (Ashmead), Fopius arisanus (Sonan), and Psyttalia incisi (Silvestri). These molecular-based findings reconfirmed the parasitoid species of B. papayae as recorded by previous studies based on morphology. In fact, the identification of Opiinae individuals have been reconfirmed based on topology and branching pattern of the phylogenetic tree as well as based on genetic distance analyses, which matched morphological-based identification.