Despite strong historical biogeographical links between benthic faunal assemblages of the Magellan region of South America and the Antarctic Peninsula, very few studies have documented contemporary movement and gene flow in or out of the Southern Ocean, especially across the Antarctic Polar Front (APF). In fact, oceanographic barriers such as the APF and Antarctica’s long geologic isolation have substantially separated the continents and facilitated the evolution of endemic marine taxa found within the Antarctic region. The Southern Ocean benthic sea slug complex, Doris ‘kerguelenensis’, are a group of direct-developing, simultaneous hermaphrodites that lack a dispersive larval stage. To date, there are 59 highly divergent species known within this complex. Here we provide evidence to show intraspecific genetic connectivity occurs across the Antarctic Polar Front for multiple species within the Doris ‘kerguelenensis’ nudibranch species complex. We addressed questions of genetic connectivity by examining the phylogeographic structure of the three best-sampled Doris ‘kerguelenensis’ species and another three trans-Antarctic Polar Front species using the protein coding mtDNA gene, Cytochrome Oxidase I. We also highlight alternative refugia uses among species with the same life history traits (i.e., benthic, direct developers) and for some species, extremely large distributions are established (e.g., circumpolarity). By improving our sampling of these nudibranchs, we gain better insight into the population structure and connectivity of the Antarctic region. This work also demonstrates how difficult it is to make generalisations across Antarctic marine species, even among ecologically-similar, closely-related species.