Continental drift processes such as major gateways openings have been historically advocated to explain the distribution of marine benthic taxa in the Southern Ocean (SO). In this respect, the separation between Antarctic Peninsula and the southern tip of South America together with the onset of the Antarctic Circumpolar Current (ACC) represent the final step for the complete isolation of the Antarctic region. However, there is still controversy concerning the timing and mode of this process, and especially about the role of the Scotia Arc geodynamics in the development of a fully deep and intensified ACC circulation. Based on mitochondrial Cytochrome c Oxidase Subunit I (COI) sequences obtained from different taxa, we performed molecular comparisons between Antarctic and South American relatives to provide independent time estimations of Antarctica's isolation. For this purpose, we include in the analyses congeneric Antarctic and Patagonian species of the genus Nacella (patellogastropoda) and Sterechinus (echinoid). We also performed comparisons between Antarctic and Patagonian populations of the nominal species Yoldia eightsii (bivalve) and Parbolasia corrugatus (nemertean). Finally, we also include in the analyses molecular comparisons between Antarctic (Trophonella) and Patagonian (Xymenopsis) muricid gastropods. Four of the analyzed groups are characterized by the presence of a dispersive larval phase (Nacella, Sterechinus, Yoldia, and Parbolasia), while Trophonella and Xymenopsis are direct developers with absence of a free-living dispersive stage. Considering the levels of genetic differentiation between relatives from both regions and assuming the molecular clock hypothesis, we estimated the onset of their respective divergence. On one hand, similar levels of genetic distance in species that develop through a free-living larval stage (broadcast-spawner) belonging to different phyla (7% - 8.3%) support the hypothesis that the development of an effective barrier between Antarctica and South America occurred almost simultaneously for these groups. Moreover, divergence time estimations based on specific substitution rates indicate that the separation occurred near the Mio-Pliocene transition, long after the physical separation of both continents. Considering that in broadcast-spawners connectivity between geographically distant areas is mainly through passive dispersal of larval stages, the onset of their divergence should be related to the installation of an effective oceanographic barrier, possibly through the intensification of the ACC. Genetic distance and divergence time estimation in a direct developer lacking of a free larval stage (brooder) muricid gastropod indicate an older separation time, close to the mid-Miocene. Even when the analyzed groups included both broadcast-spawners and brooder organisms, the divergence between Antarctic and South America lineages rather than being related to processes of continental drift, seems to be associated more to major changes in the Southern Ocean such as the evolution of the Scotia Arc and the deepening of Drake Passage. Accordingly, these results support a genetic continuity between Antarctica and South America, probably along the Scotia Ridge, until the middle Miocene and a late ACC intensification at the Mio-Pliocene boundary.