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Background: Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). The species is also admired as a landscape plant with high developmental prospects and scientific research value. The A. truncatum chloroplast genome has recently been reported; however, the mitochondrial genome (mitogenome) is still unexplored.Results: We characterized the A. truncatum mitogenome, which was assembled using reads from Pacbio and Illumina sequencing platforms, and performed a comparative analysis against different species of Acer. The circular mitogenome of A. truncatum has a length of 791,052 bp, with a base composition of 27.11% A, 22.21% T, 22.79% G, and 22.89% C. The A. truncatum mitogenome contains 62 genes, including 35 protein-coding genes, 23 tRNA genes, and 4 rRNA genes. We also examined codon usage, sequence repeats, RNA editing, and selective pressure in the A. truncatum mitogenome. To determine the evolutionary and taxonomic status of A. truncatum, we conducted a phylogenetic analysis based on the mitogenomes of A. truncatum and 25 other taxa. We also analyzed gene migration from chloroplast and nuclear genomes to the mitogenome. Finally, we developed a novel NAD1 intron indel marker for distinguishing several Acer species. Conclusions: In this study, we assembled and annotated the mitogenome of A. truncatum, a woody oil-tree species producing nervonic acid. The results of our analyses provide comprehensive information on the A. truncatum mitogenome, which should facilitate evolutionary research and molecular barcoding in Acer.