We sequenced complete mitochondrial genome of Turritopsis dohrnii. Duplicated cox1 gene and polymorphic regions were found in the linear mt chromosome. T. dohrnii has unique changes in the tertiary structures of proton-pumping proteins. Intra- and interspecific diversity was compared among various cnidarian species. Filifera IV was recovered as a polyphyletic group using mixed phylogenetic markers.