Several species within the fruit fly genus Bactrocera (Diptera: Tephritidae) are serious pests of cultivated fruit. The number of species within the genus and the relationships among them are not well understood. Therefore, we inferred phylogenetic relationships among thirty-nine Bactrocera species from 1819 base pairs of portions of the mitochondrial 16S rRNA, 12S rRNA, NADH 1 dehydrogenase, and cytochrome oxidase II + tRNA-Lys + tRNA-Asp genes. Maximum parsimony analysis suggested the following relationships: (1) Bactrocera is monophyletic, (2) B. (Zeugodacus) is polyphyletic, (3) B. (Daculus) is a sister group to B. (Bactrocera), (4) B. (Bactrocera) is monophyletic, and (5) the B. (B.) dorsalis complex is polyphyletic. Character evolution, biogeography, and male-lure response were evaluated in a phylogenetic context by mapping selected character states onto the parsimony tree. Our mapping analysis suggested that in most cases the morphological characters exhibit a simple evolutionary transition from one character state another. Within the subgenus B. (Bactrocera) four distinct clades were identified which correlated with geographic distribution. Male-lure response was identified as being a labile behavior that has been lost on multiple occasions. Cue-lure response was plesiomorphic to methyl-eugenol response and the latter has evolved independently within the Bactrocera and Zeugodacus groups. The implications of our results toward a coherent, consolidated classification for Bactrocera are discussed.