The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a comprehensive SO microbial genes collection from 218 metagenomes sampled during the Antarctic Circumnavigation Expedition, the majority of which are missing from functional databases. 38% even lack homologs in current reference marine gene catalogs, defining a singular genetic seascape. We show that SO gene assemblages exhibit a common polar signature with the Arctic Ocean while being structured by water masses at the SO-scale. We analyze genomic markers of diverse SO biomes, focusing on adaptations to organic matter consumption in the blooming Mertz polynya and temperature-dependent trace metal utilization by the ubiquist Bacteria Pelagibacter. Our work takes a step towards a more comprehensive understanding of SO’s plankton ecology and evolution, capturing the current state of the unique microbial diversity in this rapidly changing Ocean.