True fruit flies (Diptera: Tephritidae) are among the most destructive agricultural pests in the world. Because of their widespread agricultural impact and rapid range expansions, tephritids are the subject of quarantine and control efforts worldwide. There are >450 genera and 4,300 described species within Tephritidae worldwide, making it one of the largest families within Diptera. The genera Anastrepha, Bactrocera, Ceratitis, Dacus and Rhagoletis are the most important economically because many species in these genera are frugivorus. The primary aim of this study was to determine relationship among the selected species of Bactrocera using nucleotide sepquence data from both the nuclear and mitochondrial genes. The implications of results to provide a better resolved and more robust hypothesis of Bactrocera species phylogeny than did separate analyses of the individual genes is discussed.