The cynoglossid fishes are popular for food in the world including Korea, China and
Japan, and among them, Paraplagusia japonica lives all over the sea of Korea. In order to establish
appropriate management measure, it is essential to clarify population structure of P. japonica from
the morphological and molecular perspectives. We collected a total of 132 individuals of P. japonica
from six localities in Korea between 2008 and 2021. Canonical discriminant analysis results showed
that the West Sea population (Incheon) slightly differed from the South (Tongyeong, Busan) and East
Sea populations (Pohang, Donghae, Sokcho). Similar results were also shown in Kruskal-Wallis test
of meristic characters. Furthermore, neighbor-joining and maximum-likelihood trees based on 849
base pairs of mitochondrial DNA cytochrome b sequences showed that P. japonica was divided into
two lineages (designated as A and B) with a high significance (Φst=0.0781, P<0.001). Interestingly,
however, the two lineages in the admixture area (South-East Sea) were not different in morphological
characters. Our results suggest that P. japonica had undergone differentiated history during the Late
Pleistocene, but secondary contact may occur at the admixture area.