In September 2011, Aberdeen (UK) hosted the World Conference on Marine Biodiversity (WCMB). Within this Conference, the multidisciplinary international Science Research Programme (SRP) of the Scientific Committee on Antarctic Research (SCAR) “Evolution and Biodiversity in the Antarctic — The Response of Life to Change (EBA)” was granted a generous platform, which included a full-day Side Meeting on Advances in Evolution and Biodiversity in Marine Antarctic Environments. To mark the importance of this subject, as an outcome of the WCMB we decided to promote an EBA Special Issue of Marine Genomics, focussing on marine biodiversity in the polar regions. The contributions in this issue address the role of environmental change, variability and extreme events in the biological processes of marine organisms, including subjects such as phylogeography, phylogeny, phenotypic plasticity and molecular/physiological adaptations in the vertebrates and invertebrates of both polar oceans.