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The long-legged fly Rhaphium baihuashanum Yang belongs to the subfamily Rhaphiinae of Dolichopodidae. The mitogenome of R. baihuashanum was sequenced, the first representative of the mitogenome of the subfamily. The mitogenome is 15,173 bp totally, consisting of 13 protein-coding genes, two rRNAs and 22 transfer RNAs. All genes have the similar locations and strands with that of other published species of Dolichopodidae. The nucleotide composition biases toward A and T, which together made up 74.1％ of the entirety. Bayesian inference analysis strongly supported the monophyly of Dolichopodidae. It suggested that Rhaphiinae is the sister group to the clade of ((Hydrophorinae + Neurigoninae) + (Sciapodinae + Dolichopodinae)).