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.