The complete mitochondrial genome of the extinct musk ox Bootherium bombifrons is presented for the first time. Phylogenetic analysis supports placement of Bootherium as sister to the living musk ox, Ovibos moschatus, in agreement with morphological taxonomy. SNPs identified in the COI-5p region provide a tool for the identification of Bootherium among material, which is not morphologically diagnosable, for example postcrania, coprolites, and archaeological specimens, and/or lacks precise stratigraphic control, like many from glacial alluvium and in placer mines.

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