Abstract
The blue whale is an endangered and globally distributed species of baleen whale with multiple described subspecies, including the morphologically and genetically distinct pygmy blue whale. North Atlantic and North Pacific populations, however, are currently regarded as a single subspecies despite being separated by continental land masses and acoustic call differences. To determine the degree of isolation among the Northern Hemisphere populations, 14 North Pacific and 6 Western Australian blue whale nuclear and mitochondrial genomes were sequenced and analysed together with 11 publicly available North Atlantic blue whale genomes. Population genomic analyses revealed distinctly differentiated clusters and limited genetic exchange among all three populations, indicating a high degree of isolation between the Northern Hemisphere populations. Nevertheless, the genomic and mitogenomic distances between all blue whale populations, including the Western Australian pygmy blue whale, are low when compared to other inter‐subspecies distances in cetaceans. Given that the Western Australian pygmy blue whale is an already recognised subspecies and further supported by previously reported acoustic differences, a proposal is made to treat the two Northern Hemisphere populations as separate subspecies, namely Balaenoptera musculus musculus (North Atlantic blue whale) and Balaenoptera musculus sulfureus (North Pacific blue whale). Furthermore, a first molecular viability assessment of all three populations not only found a generally high genomic diversity among blue whales but also a lack of alleles at low frequency, non‐neutral evolution and increased effects of inbreeding. This suggests a substantial anthropogenic impact on the genotypes of blue whales and calls for careful monitoring in future conservation plans.