摘要The traditional knowledge in textbooks indicated that cephalochordates were the closest relatives to vertebrates among all extant organisms. However, this opinion was challenged by several recent phylogenetic studies using hundreds of nuclear genes. The researchers suggested that urochordates, but not cephalochordates, should be the closest living relatives to vertebrates. In the present study, by using data generated from hundreds of mtDNA sequences, we revalue the deuterostome phylogeny in terms of whole mitochondrial genomes (mitogenomes). Our results firmly demonstrate that each of extant deuterostome phyla and chordate subphyla is monophyletic. But the results present several alternative phylogenetic trees depending on different sequence datasets used in the analysis. Although no clear phylogenetic relationships are obtained, those trees indicate that the ancient common ancestor diversified rapidly soon after their appearance in the early Cambrian and generated all major deuterostome lineages during a short historical period, which is consistent with "Cambrian explosion" revealed by paleontologists. It was the 520-million-year's evolution that obscured the phylogenetic relationships of extant deuterostomes. Thus, we conclude that an integrative analysis approach rather than simply using more DNA sequences should be employed to address the distant evolutionary relationship.