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The long-legged fly Syntormon pallipes belongs to the subfamily Sympycninae of Dolichopodidae. The mitogenome of S. pallipes was sequenced as the first representative of the subfamily. The mitogenome is 15,583 bp long, consisting of 13 protein-coding genes, 2 rRNAs, and 22 transfer RNAs. Syntormon pallipes has the similar gene structures with other published species of Dolichopodidae. The nucleotide composition biases toward A, and T is 78.1% of the entirety. Bayesian inference analysis strongly supported the monophyly of Dolichopodidae, which was inferred from 14 species. It indicated that Sympycninae and Hydrophorinae were assigned to be the sister of the clade of ((Rhaphiinae + Neurigoninae) + (Dolichopodinae + Sciapodinae)).