Fruit flies (Diptera: Tephritidae) possess high diversity and globally wide distribution, including a range of important agricultural pests. However, the origin, phylogeny and divergence history remain poorly understood. We undertook the first comprehensive mitogenomic study covering phylogenetic reconstruction, divergence time estimation and historical biogeography analyses by analyzing 147 mitochondrial genomes representing three subfamilies, seven tribes, 11 genera and 82 species. The results recovered all the three subfamilies, seven tribes and 11 genera as monophyletic group. Within Dacini subfamily, our phylogeny strongly supported the sister group relationship of (Zeugodacus + Dacus) + Bactrocera, which further supported to raise Zeugodacus as generic level of Dacini. On the other hand, our molecular phylogenetic analyses did not align well with the currently recognized subgeneric designations within Ceratitis, Dacus and Zeugodacus. Some subgenera were recovered as polyphyletic or paraphyletic, implying the incongruence between morphological characters and mitogenomic data. Neither the taxa within the Ceratitis FARQ complex nor those within the Bactrocera dorsalis complex could be clearly distinguished as distinct species corresponding to the morphospecies by mitochondrial phylogenetic tree. Divergence time estimation and historical biogeography analyses indicated that the earliest common ancestor of the Tephritidae, originated in the Palearctic realm at 138.92-71.44 Ma, with the subsequent divergence into Dacinae + Trypetinae and Tephritinae at 115.19-67.45 Ma equally in the Palearctic realm. Dacini might have originated in Laurasia rather than Gondwana and diverged into Bactrocera and Dacus + Zeugodacus at 48.43-28.70 Ma after India plate docked with Laurasia.