The complete mitochondrial genome of the pelagic thresher Alopias pelagicus is first presented in this study. It is 16,692 bp in length and contains the 37 genes and 1 control region with the typical gene order and transcriptional direction in the vertebrates. The overall base composition is 32.1% A, 29.3% T, 25.3% C and 13.3% G. Totally, 27 bp overlaps and 25 bp short intergenic spaces are dispersal in the mitogenome. The tRNA-Ser2 (GCU) cannot be folded into the typical cloverleaf structure because of lacking the dihydrouridine arm. Two start codons (ATG and GTG) and three stop codons (AGG, TAG and TAA/T) were used in the 13 protein-coding genes.