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The Eurasian Hobby Falco subbuteo is a Falco bird belonging to the group Falconiformes, and was listed in Appendices II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora and listed as a Class II protected species on China's List of Wildlife under Special State Protection. In this study, the complete mitogenome of F. subbuteo was determined. The mitochondrial DNA is packaged in a compact 17,678 based pair (bp) circular molecule with A + T content of 54.70%. It contains 37 typical mitochondrial genes, including 13 protein-coding genes, 2 rRNAs and 22 tRNAs, and 2 non-coding regions (D-Loop). We reconstructed a phylogenetic tree based on mitogenome sequences of 13 Falconidae species and one outgroup. Phylogenetic analysis indicated that F. subbuteo was a sister taxon to F. cuvierii with node support 100. The new mitogenome data would provide useful information for application in conservation genetics and further clarify the phylogenetic evolution of this species.