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Salix cardiophylla was a member of the genus of Salix in family Salicaceae with unique morphological traits, and once recognized as a separate genus, Toisusu Kimura. Here, we sequenced and assembled the complete mitochondrial genome of S. cardiophylla, which was 735,173 bp in length, including 56 genes, 28 protein-coding genes, 3 rRNA genes, 25 tRNA genes, and one large inverted repeat regions with length of 13,603 bp. Phylogenetic analysis based on 26 mitochondrial CDS confirmed that S. cardiophylla is a member of Salix, and support its merge into Salix in aspect of our new insights on mitogenome phylogenomics.