A new species of the marine gastrotrich taxon Thaumastoderma is described. A single specimen of this species, Thaumastoderma antarctica sp. nov., was extracted from silty sediment sampled at one station of the Andeep-1 cruise, about 150 km to the north of the South Shetland Islands (Drake Passage, South Atlantic Ocean). This paper provides the first record of this genus from the deep sea and the second description of a macrodasyid gastrotrich living in an abyssal habitat. The new species is characterized by several apomorphic features, among them a caudal pair of strongly elongated dorsal cirrata tubes. A phylogenetic analysis of the genus Thaumastoderma reveals that Th. antarctica is closely related to Th. coronarium and Th. appendiculatum. Furthermore, the analysis offers an evolutionary scenario and a hypothesis for the internal phylogeny of this taxon while supporting its monophyly. It is the first time a cladistic analysis has been conducted for a delimited group of gastrotrichs, i.e. for all known members of a genus.