Aim: The Antarctic Circumpolar Current (ACC) connects benthic populations by transporting larvae around the continent, but also isolates faunas north and south of the Antarctic Convergence. We test circumpolar panmixia and dispersal across the Antarctic Convergence barrier in the benthic sea star Glabraster antarctica. Location: The Southern Ocean and south Atlantic Ocean, with comprehensive sampling including the Magellanic region, Scotia Arc, Antarctic Peninsula, Ross Sea, and East Antarctica. Methods: The cytochrome c oxidase subunit I (COI) gene (n = 285) and the internal transcribed spacer region 2 (ITS2; n = 33) were sequenced. We calculated haplotype networks for each genetic marker and estimated population connectivity and the geographic distribution of genetic structure using ΦST for COI data. Results: Glabraster antarctica is a single circum-Antarctic species with instances of gene flow between distant locations. Despite the homogenizing potential of the ACC, population structure is high (ΦST = 0.5236), and some subpopulations are genetically isolated. Genetic breaks in the Magellanic region do not align with the Antarctic Convergence, in contrast with prior studies. Connectivity patterns in East Antarctic sites are not uniform, with some regional isolation and some surprising affinities to the distant Magellanic and Scotia Arc regions. Main conclusions: Despite gene flow over extraordinary distances, there is strong phylogeographic structuring and genetic barriers evident between geographically proximate regions (e.g., Shag Rocks and South Georgia). Circumpolar panmixia is rejected, although some subpopulations show a circumpolar distribution. Stepping-stone dispersal occurs within the Scotia Arc but does not appear to facilitate connectivity across the Antarctic Convergence. The patterns of genetic connectivity in Antarctica are complex and should be considered in protected area planning for Antarctica.