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The mitochondrial genome of Gymnopternus bomiensis (Yang, ) (Diptera: Dolichopodidae) has been reported in this study. This is the first mitogenome representative of Gymnopternus. The sequenced region is determined to be 15,212 bp, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a partial A-T rich region. The nucleotide composition biased toward A and T, and the overall A + T% was up to 74.0％. Additionally, we reconstructed the phylogeny of relative species using 13 PCRs and two rRNAs. Bayesian inference analysis strongly supported the monophyly of Dolichopodinae. It also suggested that Gymnopternus is the sister group of Dolichopus.