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Malus sieversii (Rosaceae), a wild apple tree occurred in China’s Xinjiang province, is considered to be the ancestor of the modern cultivated apple. However, information on the chloroplast (cp) genome of this species is limited. With this study, we produced the first cp genome of M. sieversii using genome skimming. The whole cp genome was 163,230 bp long and comprised 128 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The M. sieversii cp genome had a GC content of 35.6%. Phylogenetic analysis showed that M. sieversii was deeply nested within the Malus clade. This study will be useful for future studies on conservation genetics and potential applications in apple breeding.