Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record

► We determine mitochondrial genomes of seven octocorals and two scyphozoans. ► We reconstruct a cnidarian tree based on 48 cnidarian mitochondrial genome data. ► We estimate divergence times of deep nodes of cnidarians. ► The time of the MRCA of Cnidaria is estimated about 741 Ma prior to the Cambrian. ► The Permian-Triassic mass extinction has impacted greatly on the evolution of corals.