DNA barcoding is a valuable tool for biodiversity studies in the Southern Ocean. It can be combined with other types of systematics data (morphology, other sequence markers) to reassess the taxonomy of complex groups and reliably delineate species. It can serve as a precise identification tool for fisheries, ecology or large scale biodiversity surveys. The rise of Next Generation Sequencing (NGS) techniques in the last 15 years has provided exciting new developments in classical barcoding identification projects like fisheries identification control, benthic biodiversity survey and voucher-linked reference datasets creation, but also new possibilities like extension of barcoding to the whole mitogenomes and to communities through metabarcoding biodiversity surveys. We provide here some examples.