In this paper, we discuss the geographical isolation and population dynamics of the largehead hairtail () populations in the East China Sea (ECS), Yellow Sea (YS), and Bohai Sea (BS). The results showed that only two largehead hairtail populations exist in the nearshore regions of the ECS, YS, and BS. The largehead hairtail population in the Northern Yellow Sea and Bohai Sea was designated as the Yellow Sea and Bohai Sea population (YSBSP), and the other population in the South Yellow Sea and the East China Sea was designated as the East China Sea population (ECSP). By evaluating moving images of largehead hairtail, we found that the YSBSP rear-ended the population in Jiangsu's northern nearshore waters at 34°00'N, 121°00'E. However, the largehead hairtail output from the overlapping waters accounted for only 1.16% of the total output. The two populations shared the same overwintering ground, and so these populations were mixed in the offshore waters to the west of Cheju Island. Only 1.16% of the total output was fished during the month in which the two populations mixed. We present six lines of evidence that there are two main populations of largehead hairtail in the studied waters. First, the output of largehead hairtail from the overlap waters is small, accounting for less than 5.51% of the total output in the same month. Second, the two groups do not produce hybrids when in overlapping waters because each group follows its own migratory route back to its wintering grounds. Third, the groups of largehead hairtail only mix in overlapping waters and not in spawning grounds, which is another reason why hybridization between the two populations is unlikely. Fourth, the two populations show different trends in their quantitative dynamics; for example, the outputs differ markedly between the two populations, suggesting that the ECSP did not contribute to the YSBSP in recent years. Fifth, there is significant geographical isolation between YSBSP and ECSP, except those in the overlapping waters. Sixth, the two different populations of largehead hairtail showed different migration patterns. Together, all of these results indicate that largehead hairtail inhabiting the East China Sea, Yellow Sea, and Bohai Sea belong to two different populations:the Yellow Sea and Bohai Sea population, and the East China Sea population.