We present the almost complete (16,007 bp) mitochondrial genome of a Colossendeis megalonyx specimen from the Southern Ocean and discuss gene order and tRNA structure in a comparative phylogenetic context. Our data suggest a basal position of the colossendeid lineage corroborating earlier phylogenetic studies but disagreeing with results of a recently published study that supported a highly derived sister-group relationship of Colossendeidae and Nymphonidae. Our results, together with BLAST searches and phylogenetic comparisons, indicate that the specimen presented as Colossendeis sp. in a series of recent studies had been misidentified. It has now been identified as a nymphonid species.