We describe the complete mitochondrial genomes of the flapper skate
Dipturus intermedius
(Parnell 1837) and the longnose skate
Dipturus oxyrinchus
(Linnaeus 1758), which have been obtained by Sanger sequencing. We report the length of the sequences to be 16,906 and 16,911 bp, respectively. The length and structure of gene regions, containing 13 protein-coding regions, 22 tRNA genes, two rRNA genes, and two non-coding areas, resemble those of related skate species. Despite
D. intermedius
being considered a cryptic species with
D. batis
, the full mitogenomes confirm that
D. intermedius
and
D. oxyrinchus
are more genetically similar. In comparison to other
Dipturus
species,
D. intermedius
is missing a whole codon in its cytochrome oxidase subunit 2 gene. These mitogenomes will be a useful resource furthering investigation of the population genetic differences and evolutionary history of skate species.