Deuterostomia, one of the three major lineages of Bilateria, comprises many well-known animals such as vertebrates, sea squirts, sea stars and sea urchins. Whereas monophyly of Deuterostomia and several subtaxa is well supported, the relationships of these to each other and, hence, deuterostome relationships are still uncertain. To address these issues in deuterostome phylogeny we analyzed datasets comprising more than 300 complete deuterostome mitochondrial genomes. Based on sequence information, the results revealed support for several relationships such as a basal position of Xenoturbella within Deuterostomia or for taxa like Craniota or Ambulacraria, but yielded also problems in some taxa, e.g. Tunicata, Pterobranchia and Ophiuroidea, due to long-branch artifacts. However, within tunicates the relationships are well supported. Variation in the genetic code was also informative and, e.g., supported the taxon Ambulacraria including Pterobranchia.