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The complete mitochondrial genome of Melanostoma scalare was sequenced and reported here. The circle genome of the syrphid fly is 16,380 bp in length. There are 38 sequence elements including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. The order of all elements was the same with that of Eristalia cerealis. With 2 species from Muscidae and Drosophilidae as outgroups, phylogenetic relationships of 8 Syrphidae species based on mitogenomes were in complete agreement with their taxonomic relationships based on morphological characteristics. Our result will provide more fundamental data to the development of the molecular systematics of Syrphidae.