The mottled skate Beringraja pulchra, distributed in the western North Pacific, is a commercially important species, directly targeted by Japanese and Korean fisheries. Despite a recently decreasing catch rate, no studies of population structure, crucial to sustainable fisheries management and conservation practices, are known to have been made. Because skates generally have low dispersal ability and are likely to have an extensive population structure, due to large benthic egg capsules and no pelagic larval stage, the population structure of the species was assessed on the basis of sequence variations of the mitochondrial DNA cytochrome c oxidase subunit I (COI) 592 bp (in 166 individuals) and morphological variations in seven morphometric characters (in 192 individuals), representing five areas, including Hokkaido, Japan [coasts along Sea of Okhotsk, Pacific Ocean, and Sea of Japan (the East Sea of Korea)], western Sea of Japan, and Yellow Sea. The genetic analysis detected 12 haplotypes, six being shared among the sampling areas, although significant pairwise ΦST estimates indicated restricted gene flow among the sampling areas (excluding those off the Hokkaido). The extensive population structure of the species was also supported by morphological differences in several characters, such as disc length, disc width, and eye diameter. Beringraja pulchra was concluded as being clearly structured into three populations for future management, viz. Hokkaido, western Sea of Japan, and Yellow Sea populations. This population structure may have been shaped by the Tsushima Current flowing between the Korean Peninsula and the Japanese Archipelago, the species generally inhabiting colder water.