The complete mitochondrial genome of the Reef Manta Ray, Mobula alfredi, from Hawaii.

We provide the complete mitochondrial genome of the reef manta ray, Mobula alfredi, using an ezRAD approach. The total length of the mitogenome was 18,166 bp and contained 13 protein-coding genes, 22 transfer RNAs genes, two ribosomal RNA genes, and one non-coding control region. The gene organization and length are similar to other Mobula species. This reference mitogenome that includes the control region is expected to be a valuable resource for molecular-based species identification, population genomics, and phylogeography.