The rock bream, Oplegnathus fasciatus, is a common rocky reef game fish in East Asia and recently becomes an aquaculture species. Although being commercial and economically important species, the population genetic structure remains poorly understood. In the current study, one hundred and sixty-three specimens have been collected from 6 localities along the coastal waters of Korea and China including Kangnung (KN; East Sea), Goseong (GS; Korea Strait), Heuksando (HS; Yellow Sea), Ieodo (ID; Ieodo Ocean Research Station of Korea), Jiaonan (JN; Yellow Sea), and Zhoushan (ZS; East China Sea near China/Taiwan) to analyze population genetic variation of the species using mitochondrial DNA COI sequences. A total of 34 polymorphic sites were detected and 30 haplotypes were defined. The genetic diversity of O. fasciatus shows a pattern of low level of nucleotide diversity (0.04±0.003) and high level of haplotype diversity (0.83±0.02). The individuals from Zhoushan (ZS) in the East China Sea near China/Taiwan presented the highest genetic diversity in terms of nucleotide diversity (0.009±0.005), haplotype diversity (0.81±0.06), and average pairwise nucleotide differences (5.65±2.79) among the six groups. Two major genealogical clades were identified in the 30 haplotypes through Bayesian and statistical parsimony analyses, and the net genetic distance between two clades were 0.018±0.004 nucleotide difference per site. The analyses of the AMOVA, Fst, and the exact p test yielded a significant population differentiation between the Zhoushan group and the rest of the populations. Neutrality tests and mismatch distribution analyses indicated recent population expansion of the species inhabiting the coastal waters of Korea and China approximately 133-183 kyr before present. The results suggest that the East Asian rock bream was divided into the north and south populations having the mouth of the Yangtze river as a boundary and has experienced demographic expansion at the late Pleistocene. Such population genetic structure needs to be considered in the establishment of the stock management strategies for this fisheries species.