The glacial cycles of the Pleistocene have promoted the principal climatic changes of the Southern Ocean, and motivated scientific interest regarding the strategies developed by marine benthic invertebrates to tolerate and overcome the extension and contraction of the ice sheet on the Antarctic continental platform. A recent study of the bathymetric zonation and distribution of macro-invertebrates in a shallow subtidal area of Fildes Bay (King George Island, South Shetlands Islands, Antarctica) highlighted the presence of a large aggregation of the brooding sea urchin Abatus agassizii, whose geographic distribution is known only for localities south of the Antarctic convergence (Antarctic Peninsula and South Shetland and South Georgia Islands in the Scotia Arc). Its presence is atypical, given that these shallow populations should have been erased from the vicinity of the Antarctic Peninsula by the advances and retreats of the ice sheet, and the absence of a larval stage associated with brooding should limit re-colonization from northern Subantarctic areas. The aim of the study was to evaluate whether A. agassizii may have survived the glaciations in its narrow bathymetric range in the South Shetland Islands, or whether this population corresponds to a newcomer that re-colonized the area despite its low dispersal capacities. For this, we combined multidisciplinary approaches based on the geographical distribution of A. agassizii, its genetic diversity and its phylogenetic relationships with other species of the genus. In spite of an intensive sampling effort, the low occurrence of A. agassizii indicated that its distribution is very scarce along the Shetlands Islands and the Antarctic Peninsula, and seems to be restricted to protected and ice-free areas of Fildes Bay in King George Island. Moreover, this population presented very low genetic diversity associated with the signal of a recent demographic expansion. Finally, the reconstruction of the phylogenetic relationships among species of Abatus using mitochondrial COI sequences established the affinity of the Antarctic A. agassizii with Subantarctic species. Based on these results we consider that the presence of this species in the Shetland Islands more likely corresponds to a recent re-colonization from Antarctic Islands located further north.