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Malus kansuensis, which belongs to the family Rosaceae, is an important apple rootstock resource in China. In the present study, the mitochondrial genome of M. kansuensis was sequenced and assembled by high-throughput sequencing (HTS). The genome was 385,436 bp in length, with an obvious (A + T) % bias over (G + C) %. The mitochondrial genome comprised 35 protein-coding genes, 21 tRNA genes, and 3 rRNA genes. The phylogenetic tree results showed that M. kansuensis is very close to M. domestica and M. hupehensis.