Abstract <p>Exploring in traspecific patterns of genetic differentiation is crucial for biodiversity conservation and adaptive evolution. The spotted seal (<i>Phoca largha</i>) is an important flagship marine mammal and umbrella species in the North Pacific Ocean, yet few studies have investigated the genetic differentiation patterns of this species throughout its wide distribution range. Here, comparative mitogenomics approaches were conducted to analyze genetic differentiation and evolutionary patterns of the spotted seal. Mitogenome size variation (16 549–16 774 bp) and high-level genetic differentiation were revealed, which were mainly attributed to the tandem repeats detected in the control region. A total of five types of repeat units and a maximum repetition of 27 were observed in the control region, among which “TACACG” was suggested to be the ancestral unit. Phylogenetic analyses revealed that the individual from Alaska was at the basal position. In addition, our results uncovered that observed tandem repeats in the control region should be the key contributor to intraspecific genetic differentiation of the spotted seal. In future studies, additional mitogenome sequences from diverse geographic populations are needed to elucidate the evolutionary origin and possible functional consequences of the observed tandem repeats in the mitochondrial control region of the spotted seal.</p>