The melon fly, Zeugodacus cucurbitae (Diptera:Tephritidae) is an important invasive pest and distributed throughout tropical, subtropical countries and areas. In this study, we report the complete mitochondrial genome of the fly with 15, 685 base pair in length, which includes 37 genes (the large and small ribosomal RNA subunits, 22 transfer RNA genes, 13 genes encoding mitochondrial proteins) and a noncoding A þ T-rich control region. Molecular phylogeny indicated that there was a high bootstrap value supported among Z. cucurbitae and Z. tau belonging to the Z. tau complex.

The black-winged fly, Felderimyia fuscipennis (Diptera: Tephritidae), is an insect pest of bamboo shoot, mainly distributed in Thailand, Malaysia and Yunnan Province and Guangxi Autonomous Region, China. The complete sequence of the mitogenome of F. fuscipennis has been determined in this study. The whole mitogenome sequence is 16,536 bp in length, which totally contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding region (putative control region, CR). The phylogeny indicates that F. fuscipennis of subfamily Trypetinae was monophyletic and clearly separated from both Dacinae and Tephritinae with high bootstrap value supported.

Zeugodacus tau (Walker) (Diptera: Tephritidae), is widely distributed throughout South and Southeast Asia. complete sequence of the mitogenome of Z. tau has been determined in this study. The circular genome is 15830 bp long and contains a standard gene complement, that is, the large and small ribosomal RNA subunits, 22 transfer RNA genes, 13 genes encoding mitochondrial proteins, and a non-coding A þ T-rich control region. The phylogeny showed that Z. tau is closely related to Z. depressus with high bootstrap value supported and that monophyletic Bactrocera, Zeugodacus, and Ceratitidini were correctly identified within subfamily Dacinae.