The mitochondrial DNA cytochrome c oxidase subunit I (COI) gene was used to evaluate the population genetics and elaborate the historical demography of Scomber japonicus collected from four geographical locations in the Taiwan Strait and its adjacent waters. The results of genetic diversity and genetic structure analysis of S. japonicus showed that these four populations exhibited moderate genetic diversity across the sampled geographical range of the species. However, no phylogenetic structure corresponding to geographic location was observed from the neighbor-joining (NJ) tree and haplotype network analyses, and gene flow and exact P test results revealed that a wide range of gene flow occurred among the four S. japonicus populations. Analysis of molecular variance (AMOVA) and Fst analysis showed that genetic variation was mainly derived from within populations, and genetic divergence was very weak among populations. The complex hydrologic environment of the Taiwan Strait and its adjacent waters did not block gene flow among different populations, which indicates relatively high genetic homogeneity; thus, the populations should belong to the same fishery management unit. The nucleotide mismatch distribution and neutrality test results indicated that the studied S. japonicus populations experienced a recent expansion event during the late Pleistocene. At present, S. japonicus resources show recessions and decreased mean ages due to overfishing, emphasizing the need to strengthen the management of corresponding fisheries and to develop and reasonably utilize S. japonicus resources to achieve sustainable development.