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The dance fly Hybos serratus Yang et Yang belongs to the subfamily Hybotinae of Empididae. The mitogenome of H. serratus was sequenced, the first representative of the mitogenome of the subfamily. The nearly complete mitogenome is 15,997 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 Empididae. The nucleotide composition biases towards A and T, which together made up 79% of the entirety. Bayesian inference analysis strongly supported the monophyly of Empidoidea and Dolichopodidae. This result also suggested that Hybotinae is assigned to the sister group to the clade of Dolichopodidae and Empididae.