Blue whales are the largest animals that have ever lived and were hunted to the brink of extinction in the middle of the twentieth century. The blue whale (Balaenopterus musculus musculus) in the Northwest Atlantic is endangered and consists of less than 250 adults. The blue whales in the Northwest Atlantic are still under threat from anthropogenic effects. Despite the precarious conservation status of this iconic species in the North Atlantic, population dynamics, genetic structuring, and introgression are poorly understood. The Balaenopterus musculus musculus genome can help to gain insights into the population structure and dynamics of this species. The sequencing and population structuring studies can provide a genomic framework to guide ongoing conservation strategies for this sentient species.