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Arabis alpina (A. alpina) is an arctic-alpine flowering plant in the family Brassicaceae, naturally growing in the tundra of arctic regions and in mountains at southern latitudes. In this study, we first report the assembly of the complete A. alpina mitochondrial (mt) genome using the next-generation sequencing technologies. The A. alpina mt circular genome is 323,159 bp in length and contains 33 protein-coding genes, 18 tRNA genes and 3 rRNA genes. To analyze the phylogenic and evolutional relationship of A. alpina, a neighbour-joining phylogenetic tree was reconstructed based on the mt genome of A. alpina and other 27 plants. The complete A. alpina mt genome will be helpful in population studies or investigations of mt functions of these alpine plant species.