Climatic oscillations in Antarctica caused a succession of expansion and reduction of the ice sheets covering the continental shelf of the Southern Ocean. For marine invertebrates, these successions are suspected to have driven allopatric speciation, endemism and the prevalence of cryptic species, leading to the so-called Antarctic ‘biodiversity pump’ hypothesis. Here we took advantage of the recent sampling effort influenced by the International Polar Year (2007-8) to test for the validity of this hypothesis for 1,797 samples of two recognized crinoid species: Promachocrinus kerguelensis and Florometra mawsoni. Species delimitation analysis identified seven phylogroups. As previously suggested, Promachocrinus kerguelensis forms a complex of six cryptic species. Conversely, despite the morphological differences, our results show that Florometra mawsoni is a lineage nested within Promachocrinus kerguelensis. It suggests that Florometra mawsoni and Promachocrinus kerguelensis belong to the same complex of species. Furthermore, this study indicates that over time and space the different sectors of the Southern Ocean show a remarkable rapid turn-over in term of phylogroups composition and also of genetic variants within phylogroups. We argue that strong “apparent” genetic drift causes this rapid genetic turn-over. Finally, we dated the last common ancestor of all phylogroups at less than 1,000 years, raising doubts on the relevance of the Antarctic “biodiversity pump” for this complex of species. This work is a first step towards a better understanding of how life is diversifying in the Southern Ocean.