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Mitochondrial genomes provide an additional data source for nuclear phylogenomics. Recently, the taxonomic classification of Ophiuroidea was changed dramatically based on a molecular phylogenetic analysis that utilized a huge nuclear dataset of transcriptome and target-capture approaches. However, the mitochondrial genome analysis of Ophiuroidea was not conducted sufficiently in depth to allow comparison with current phylogenetic relationships, especially for the Ophintegrida. In this study, eight mitogenomes were newly reported in Amphilepidida and Ophiacanthida. Phylogenetic analyses were undertaken based on the nucleotide sequences of 13 protein coding genes (PCGs), 22 tRNA, and two rRNA, and the amino acid translated sequences of 13 PCGs. The results of the phylogenetic analysis suggested that the amino acid translated sequences were more useful than the nucleotide sequences for the analysis of higher phylogenetic relationships. The mitochondrial gene order of 13 PCGs and two rRNA in Amphilepidida and Ophiacanthida was relatively conserved. However, more complex gene orders occurred in the phylogeny of Amphilepidida and Ophiacanthida, including 22 tRNA. The results of our study suggest that Ophiuroidea has undergone more complex gene rearrangements than other classes of echinoderms. [ABSTRACT FROM AUTHOR]