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Manihot esculenta (M. esculenta) is the most important root crop in the world, which has high potential carbohydrate production and adaptability to diverse environments. In this study, we assembled the complete mitochondrial (mt) DNA sequence of M. esculenta into a circular genome of length 682,840 bp, comprising of 32 protein-coding genes, 17 tRNA genes, and three rRNA genes. A neighbour-joining phylogenetic tree was constructed based on 25 plant species and 23 conserved protein-coding genes, suggesting that M. esculenta is evolutionarily close to the Salicaceae plants (Populus tremula and Salix suchowensis) in the same Malpighiales order. The complete mt genome of M. esculenta will provide more desirable information for better understanding the genomic breeding of cassava.