Abstract: Elucidating the genetic variation patterns of fishery species is of great significance for their resource management and conservation. The blue shark (Prionace glauca), as a large pelagic migratory cartilaginous fish, has significant ecological and conservation value. However, there are few reports on its mitochondrial genetic variation pattern. In this study, we assembled and annotated the mitogenome of P. glauca collected from the coastal waters of Zhoushan, China, and conducted comparative analyses to examine its mitochondrial evolutionary patterns and phylogenetic status. Meanwhile, the phylogenetic relationships among 20 carcharhinid species were reconstructed. The newly assembled mitochondrial genome of the blue shark is 16 706 bp in length and possesses the typical features of vertebrate mitochondrial genomes. Comparative analyses revealed that: (1) The complete mitogenome assembled in this study clustered first with that from the coastal waters of Greece, indicating trans-oceanic genetic homogeneity in the blue shark; (2) A total of 58 variable sites were detected, most of which (44/58, 75.87%) were located in the protein-coding genes (PCGs), and eight were in the control region. and the genetic variability of protein-coding genes such as ND1, ND4, and ND5 was comparable to that of the control region; (3) The variable sites located in protein-coding genes were predominantly synonymous substitutions, suggesting strong purifying selection in the blue shark mitogenomes; (4) Phylogenetic analyses of 20 Carcharhinidae‌ species based on different datasets revealed extensive phylogenetic conflicts and paraphyletic relationships within the genus Carcharhinus, indicating the complexity of their phylogenetic relationships. The exceptionally high genetic variability observed in the mitochondrial protein-coding genes of the blue shark suggests that NADH dehydrogenase genes should be considered in future population genetic studies to accurately assess genetic diversity. These findings from our study provide novel implications for the management and conservation of blue shark fisheries.