The small yellow croaker (Larimichthys polyactis), which is among the most important fishery resources in the northwestern Pacific, is distributed in the Yellow Sea (YS) and East China Sea (ECS). Although many studies have analyzed effective measures for managing L. polyactis, its population structure differs depending on the type of marker. To resolve such discrepancies among markers, we analyzed the population structure of 48 L. polyactis individuals collected from three locations in the YS (off Yeonpyeong-do and Yeonggwang, Korea, and Dandong, China) and one location in the northern ECS (off Jeju Island, Korea) using multiplexed intersimple sequence repeat genotyping. A total of 58,340,434 raw reads were obtained, and 42,587,565 were identified after filtering. Phylogenetic analysis using 88,672 SNPs revealed a great distance between two Dandong individuals and individuals from the remaining locations. Two other Dandong individuals also showed slight separation. The results of structural analysis based on 3,996 SNPs demonstrated an optimal ∆K for K = 5. Three of the five genotypes appeared in all locations, and two genotypes were identified only in four individuals from Dandong. These results suggested that there may be five populations of L. polyactis from YS and ECS: two populations with limited distributions in the northern YS, and three populations tending to mix across northern YS and northern ECS (58.3-75.0%), with some showing hybridization (16.7-58.3%). Therefore, joint management between Korea and China is required for L. polyactis, and a separate policy in each country is required for the protection of local spawning grounds.

The elongate ilisha (Ilisha elongata) is a significant commercial species found along the Northwestern Pacific Coast. A sharp decline in the annual catch of I. elongata over recent decades implies a concerning situation regarding its fishery stocks. Nonetheless, inadequate knowledge of the genetic diversity, population structure, and historical demography of this species has hindered the establishment of sustainable fishery policies and appropriate conservation measures. In this study, the genetic structure and population demography of I. elongata stocks along the Northwestern Pacific Coast were examined using target-gene enrichment data from 144 I. elongata individuals collected from 18 locations. The findings reveal that with an average value of 0.2173, I. elongata maintains a notable level of nucleotide diversity despite facing considerable fishing pressure. Furthermore, inter-population differentiation is relatively low, with most geographical populations displaying minimal genetic distinctions or none from one another. Population clustering analysis identified four lineages of I. elongata stocks. Through historical demography simulations, it was proposed that the Yalu River Estuary population diverged initially around 19500 generations before present, while the remaining lineage split into two about 18800 generations ago. One lineage represents the southern population, while the other further separated into the northern population and the Japanese population approximately 3000 generations ago. These results underscore that the current phylogeographic patterns of I. elongata may result from directional selection due to low temperatures and geographic barriers during glacial periods, followed by recent expansions.