Sequence analyses on the complete mitochondrial DNA control region were conducted to elucidate the population structure and population expansion of common mackerel (Scomber japonicus) off Taiwan. Three samples including 90 individuals were collected separately from waters off Keelung (PJ), Taitung (TT) and Linyan (LY). Control region sequences of one sample from Portugal (POR) were also sequenced and compared. Haplotype diversity (h) in the total data set was 97.10±0.8%, and the variations within samples ranged from 95.6±2.7% (PJ) to 100%±4.5% (POR). Nucleotide diversity (π) in the total data set was 1.71±0.18%, and variation within samples ranged from 1.06±0.05% (PJ) to 1.11±0.18% (POR). Analyses of a neighbor-joining tree of identified DNA haplotypes and F(subscript ST) values between samples, and an analysis of molecular variance revealed significant genetic differences between samples from Portugal and Taiwan, but no differentiation among the samples from Taiwan. These results suggested that the common mackerels off Taiwan belong to the single gene pool. Both mismatch distribution analysis and neutrality test suggested common mackerel off Taiwan had experienced population expansion since the late Pleistocene.