This circumpolar dataset of the comatulid (Echinodermata: Crinoidea) Promachocrinus kerguelensis (Carpenter, 1888) from the Southern Ocean, documents biodiversity associated with the specimens sequenced in Hemery et al. (2012). The aim of Hemery et al. (2012) paper was to use phylogeographic and phylogenetic tools to assess the genetic diversity, demographic history and evolutionary relationships of this very common and abundant comatulid, in the context of the glacial history of the Antarctic and Sub-Antarctic shelves (Thatje et al. 2005, 2008). Over one thousand three hundred specimens (1307) used in this study were collected during seventeen cruises from 1996 to 2010, in eight regions of the Southern Ocean: Kerguelen Plateau, Davis Sea, Dumont d'Urville Sea, Ross Sea, Amundsen Sea, West Antarctic Peninsula, East Weddell Sea and Scotia Arc including the tip of the Antarctic Peninsula and the Bransfield Strait. We give here the metadata of this dataset, which lists sampling sources (cruise ID, ship name, sampling date, sampling gear), sampling sites (station, geographic coordinates, depth) and genetic data (phylogroup, haplotype, sequence ID) for each of the 1307 specimens. The identification of the specimens was controlled by an expert taxonomist specialist of crinoids (Marc Eleaume, Museum national d'Histoire naturelle, Paris) and all the COI sequences were matched against those available on the Barcode of Life Data System (BOLD: http://www.boldsystems.org/index.php/ IDS_OpenIdEngine). This dataset can be used by studies dealing with, among other interests, Antarctic and/or crinoid diversity ( species richness, distribution patterns), biogeography or habitat / ecological niche modeling. This dataset is accessible through the GBIF network at http://ipt.biodiversity.aq/resource.do?r=proke.