The Southern Ocean benthic communities are characterized by their levels of endemism and their diversity of invertebrate brooding species. Overall, biological processes acting within these species remain poorly understood despite their importance to understand impacts of ongoing global change. We take part in filling this gap by studying the genetic structure over different spatial scales (from centimeters to tens of kilometers) in Abatus cordatus, an endemic and brooding sea urchin from the Kerguelen Islands. We developed three microsatellites and two exon-primed intron crossing markers and conducted a two-scale sampling scheme (from individuals to patches) within two dense localities of Abatus cordatus. Between patches, all pairwise comparisons, covering distances from few meters (between patches within locality) to 25 km (between localities), revealed significant genetic differentiation, a higher proportion of the molecular variance being explained by the comparisons between localities than within localities, in agreement with an isolation by distance model. Within patches, we found no significant correlation between individual pairwise spatial and genetic distances, except for the most polymorphic locus in the patch where the largest range of geographical distances had been analyzed. This study provides an estimation of the dispersal capacities of Abatus cordatus and highlights its low recolonization ability. Similar low recolonization capacities are thus expected in other Antarctic and Subantarctic brooding invertebrate species and suggest a high vulnerability of these species facing global change.