The 17514-nucleotide mitochondrial DNA (mtDNA) sequence of the deepwater stingray (Plesiobatis daviesi) was determined using long PCR and primer walking methods. The deepwater stingray genome contains 37 genes, including 2 ribosomal RNAs, 22 transfer RNAs (tRNAs), and 13 protein-coding genes, which are similar to other vertebrates. A comparison of the deepwater stingray mtDNA sequence with that of seven completely sequenced chondrichthyan mtDNAs revealed an identical gene order. However, the major noncoding region of the deepwater stingray genome, a D-loop sequence between the tRNAPro and tRNAPhe, is the longest (1830 bp) among all known available sequences of chondrichthyan species. The components of D-loop sequences are two major copies of 47-bp tandem repeats and two characteristic conserved sequence blocks in this region. Phylogenetic analyses suggest that the deepwater stingray belongs to the basal group of Myliobatoidei that forms a sister group with Hexatrygonidae.