Phylogenetic relationships within Hexacorallia (Cnidaria, Anthozoa) have long been debated. Recently, complete mitochondrial (mt) genomes for all the hexacorallian orders have been obtained by different research groups, but no global analyses including all these data have yet been performed. Here we present the partial genome of the antipatharian Leiopathes glaberrima and the result of the first phylogenetic analyses including complete mitochondrial genomes of the five hexacorallian orders (Ceriantharia not being considered as true hexacorallian). Moreover, we report for the first time the presence of an intron in COI in the an antipatharian mt genome.