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Bactrocera (Bulladacus) cinnabaria and B. (Bactrocera) propinqua are tephritid fruit flies of the subfamily Dacinae, tribe Dacini. The whole mitogenomes of these two species (first report for the subgenus Bulladacus) possess 37 genes (13 protein-coding genes – PCGs, 2 rRNA and 22 tRNA genes). The mitogenome of B. cinnabaria (15,225 bp) is shorter than that of B. propinqua (15,927 bp), mainly due to the smaller size of the control region and intergenic spacers in B. cinnabaria. Molecular phylogeny based on mitochondrial genes (mt-genes) reveals two clades of the genus Bactrocera: one comprising the subgenus Bactrocera and the other comprising the subgenera Bulladacus, Daculus, Tetradacus and unassigned Bactrocera sp. ‘yunnanensis’. The subgenera represented by two or more taxa are monophyletic. B. (Bulladacus) cinnabaria forms a sister group with the subgenus Tetradacus (B. minax and B. tsuneonis) and B. sp. ‘yunnanensis’, in a clade containing also the basal sister lineage of the subgenus Daculus (B. oleae and B. biguttula). B. propinqua forms a sister group with B. ritsemai and B. limbifera in a subclade containing also B. umbrosa, B. curvifera and B. moluccensis of the monophyletic subgenus Bactrocera. The present study supports the synonymy of B. ruiliensis with B. thailandica. It also shows a high genetic similarity between (a) B. melastomatos and B. rubigina, (b) B. papayae and B. philippinensis, (c) B. dorsalis and B. invadens, (d) B. tryoni and B. neohumeralis, and (e) B. cheni and B. tuberculata; and B. cheni is distinct from and not a synonym of B. tsuneonis or B. lombokensis.