Southern Ocean biodiversity reflects past climate, oceanographic, and tectonic changes. Molecular data from contemporary populations carry signatures of these processes. Here, we review new molecular studies on Southern Ocean benthic fauna. Many of these studies focus on species with extensive geographic or bathymetric distributions, and resolve taxonomic questions. Reviewing all available data, we show that, in addition to reflecting life-history characteristics, the molecular signals found in these studies provide an insight into how species survived the last glacial maximum (LGM). We identify molecular signatures that are characteristic of surviving glacial cycles in small refugia on the continental shelf and distinguish them from molecular signatures that are indicative of surviving glacial cycles in the deep sea.