Blue whales are the largest living animal and became endangered due to whaling. We found three major groupings of blue whales using high-resolution population genomics: the eastern Pacific, Indo-western Pacific, and Antarctic blue whales. Within these groupings, there was divergence between the eastern North and eastern South Pacific; between the eastern Indian Ocean, the western South Pacific, and the northern Indian Ocean; and no divergence within the Antarctic. The study reinforces that population structure needs to be well understood to conserve the diversity within species. image