The purpleback flying squid Sthenoteuthis oualaniensis is widely distributed in tropical and subtropical areas of the Pacific Ocean and the Indian Ocean. In the northwest Pacific, the highest concentration is found in the South China Sea, while the waters of Ryukyu Islands and southwest Taiwan are regarded as fishing grounds of S. oualaniensis. To manage this squid and exploit it scientifically, it is important to investigate the genetic structure of its population. In this study, the genetic diversity of S. oualaniensis from the northwest Pacific (including the South China Sea, the East China Sea, and the Philippine Sea) was revealed, and sequence analysis of the mitochondrial DNA cytochrome b gene (Cytb) was used to assess its genetic structure. A total of 105 partial sequences of cytb were obtained, each 896 bp long, from which 72 haplotypes were defined. Haplotype diversities and nucleotide diversities for all geographical populations were 0.982±0.006 and 0.012±0.006, respectively, with corresponding maximum values of 0.973±0.014 and 0.015±0.008, respectively, in the population from the Philippine Sea. Haplotype diversities in populations from the South China Sea and the East China Sea were 0.959±0.026 and 0.943±0.031, respectively, while nucleotide diversities were 0.006±0.003 for both areas. Three populations from the South China Sea, the East China Sea, and the Philippine Sea were characterized by a higher haplotype diversity and higher nucleotide diversity. Analysis of molecular variance showed that 34.6% of genetic variance came from individuals among populations, and highly significant genetic differentiation was detected; a similar result was obtained from the fixation indices (F_st) among the three populations. The neighbor-joining haplotype tree and reduced median network analysis detected three distinct lineages (A, B, and C), and highly significant genetic differentiation was detected among the lineages (F_st=0.735-0.805). Neutrality tests and mismatch distribution analysis suggested that lineage B recently experienced a population expansion, around 103 000-125 000 years ago. In summary, the genetic structure and phylogeographic pattern of S. oualaniensis in the northwest Pacific appear to have been caused by ocean currents and climatic changes since the Pleistocene. The northwest Pacific S. oualaniensis should be considered as at least three stocks in their assessment and management.