Understanding patterns of contemporary population genetic structure and diversity is critically important for cold-adapted Southern Ocean benthic species along the Scotia Arc to distinguish between natural and anthropogenically-mediated range expansions and detect population declines due to the rapid climate change. We report the isolation and characterization of 10 polymorphic microsatellite loci for the Antarctic endemic giant isopod Glyptonotus antarcticus from the Eastern Scotia Arc (n = 30). The number of alleles per locus ranged from 3 to 11 with no evidence of significant linkage disequilibrium between loci. These markers will prove useful in studying the fine-scale processes, which have shaped the spatial distribution of variation, and hypothesis-testing in the Scotia Arc region of Antarctica.