The ecology of Antarctic deep-sea fauna is poorly understood and few studies have gone beyond assessing biodiversity when comparing deep regions of the Southern Ocean. Protobranch bivalves are ubiquitous in the deep ocean and are widely distributed in the Southern Ocean. This paper examines the potential respon ses to environmental differences in the common protobranchs Yoldiella valettei, Yoldiella ecaudata, and Yoldiella sabrina from contrasting deep-sea environments of the Weddell Sea, Scotia Sea, Amundsen Sea, and South Atlantic. There are significant differences in morphology between deep-sea regions in all species and a significant difference in shell weight in Y. valettei between the Amundsen Sea and Weddell Seas. Growth rates of Y. valettei and Y. ecaudata in the Amundsen Sea are also higher than elsewhere and Y. valettei have heaviest shells in the Amundsen Sea, suggesting more favourable conditions for calcification and growth. The plasticity observed among deep-sea regions in the Southern Ocean is likely to be driven by different oceanographic influences affecting temperature and food fluxes to the benthos, and demonstrate the species’ ability to differentially adapt between cold-stenothermal environments. This study suggests that subtle changes in the environment may lead to a divergence in the ecology of invertebrate populations and showcases the protobranch bivalves as a future model group for the study of speciation and radiation processes through cold-stenothermal environments.