The Late Pleistocene climate fluctuations have had a major impact on phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. The puffer fish Lagocephalus spadiceus, has high nutritional and economic value in the South China Sea. To allow the examination of the demographic history and population structure of the L. spadiceus, the mitochondrial DNA COI and Cyt b gene datasets of 300 individuals from eight populations in the South China Sea was sequenced. High haplotype diversity (0.874 ± 0.013) and low nucleotide diversity (0.00075 ± 0.00058) were observed. The phylogenetic tree and haplotypes network revealed no significant genetic differentiation along the coast of the northern South China Sea. Neutrality tests, mismatch distribution analysis, and Bayesian skyline plots suggested that L. spadiceus experienced population expansion during the Late Pleistocene. Ocean currents and climate change play important roles in shaping the geographical distribution and genetic population structure of L. spadiceus.