ABSTRACT: The population genetic structure and level of gene flow of Nibea albiflora from the Yellow Sea and the East China Sea were examined with a 479-bp segment of a mtDNA control region. In total, 65 samples were collected from three locations and 37 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the three populations ranged from 0.9130 ± 0.0308 (Zhoushan) to 0.9926 ± 0.0230 (Xiamen), and from 0.0073 ± 0.0043 (Qingdao) to 0.0099 ± 0.0057 (Xiamen). Analysis of molecular variance and pairwise FST revealed little genetic structure between the Yellow Sea and the East China Sea in N. albiflora. But based on the exact test of differentiation, the null hypothesis that N. albiflora within the Yellow Sea and the East China Sea constitutes a panmictic mtDNA gene pool was rejected. This might be caused by the broad spawning areas but not by the Yangtze River outflow. Mismatch distribution revealed that N. albiflora has undergone population expansion, possibly before the last 85 000–170 000 years. The existence of high gene flow between stocks in the studied area was supported by our results. Annual migrations, larval drift in the ocean currents, and recent range expansion could be the reasons for little genetic structure in the studied area.