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The Last Glacial Maximum climate, which severely influenced the sea level, surface water temperature and currents, combining with present marine environment and life historical characteristics, could mainly determine the phylogeographical pattern of marine species in the East China Sea and the South China Sea. Thamnaconus hypargyreus is a commercially important but intensively exploited species in the South China Sea and the East China Sea, and morphological studies indicated population variations between these two seas. Hence in our study, the control region segment of mitochondrial DNA was sequenced to detect the genetic diversity, mitochondrial phylogeographical pattern and genetic connectivity of T. hypargyreus in the South China Sea and the East China Sea. The results indicated high levels of control region diversity, lack of significant phylogeographical structure and historical population expansion after the Pleistocene. The Last Glacial Maximum marine environment, the present ocean currents and life history with high dispersal potential should be responsible for high levels of genetic connectivity among the analyzed populations and shallow phylogeographical pattern. Baselines on the genetic structure and genetic diversity would be essential for the effective conservation and sustainable fishery management. [ABSTRACT FROM AUTHOR]