This paper reviews, reanalyzes and contributes new data pertinent to understanding genetic connectivity in benthic invertebrates at differing spatial scales in Antarctica. This information is valuable for understanding the potential resilience of benthic communities under threat from bottom fishing. Genetic connectivity allows insight into the realized dispersal of organisms, i.e. the likelihood of new recruits arriving from surrounding areas. Despite the wide distribution patterns shown by many marine organisms in Antarctica, population genetics analyses indicate that benthic marine invertebrates rarely show connectivity across major regions. Even taxa that have long-lived larvae, and therefore great dispersal potential, show unexpected genetic structure. Breaks to gene flow are most likely facilitated by distance and deep-water barriers. A number of organisms exhibited genetic homogeneity within isolated island regions e.g. South Georgia, the South Orkneys, Bouvet Island. The exception to this was the Antarctic Peninsula, where the Bransfield Strait may represent a distinct region. If representative protected areas are created within areas known to house genetically distinct populations, conserving genetic diversity would be maximized. However, further thought must be given to protecting areas that might maintain genetic connectivity across major regions, which would essentially act as stepping-stones for gene flow. At present, the available data is very incomplete, and an understanding of the generality of these patterns is limited.