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Aim: To provide a method of analyzing penguin tracking data to identify priority at‐sea areas for seabird conservation (marine IBAs), based on pre‐existing approaches for flying seabirds but revised according to the specific ecology of Pygoscelis penguin species. Location: Waters around the Antarctic Peninsula, South Shetland, and South Orkney archipelagos (FAO Subareas 48.1 and 48.2). Methods: We made key improvements to the pre‐existing protocol for identifying marine IBAs that include refining the track interpolation method and revision of parameters for the kernel analysis (smoothing factor and utilization distribution) using sensitivity tests. We applied the revised method to 24 datasets of tracking data on penguins (three species, seven colonies, and three different breeding stages—incubation, brood, and crèche). Results: We identified five new marine IBAs for seabirds in the study area, estimated to hold ca. 600,000 adult penguins. Main conclusions: The results demonstrate the efficacy of a new method for the designation of a network of marine IBAs in Antarctic waters for penguins based on tracking data, which can contribute to an evidence‐based, precautionary, management framework for krill fisheries. We present a method of analyzing penguin tracking data to identify priority at‐sea areas for penguin conservation (marine IBAs). We identified five new marine IBAs for penguins breeding in South Shetland and South Orkney archipelagos, estimated to hold ca. 600,000 adult penguins. The results can contribute to an evidence‐based, precautionary, management framework for krill fisheries. [ABSTRACT FROM AUTHOR]