We analyzed stable isotope ratios, fatty acid, and lipid components of chub mackerel, Scomber japonicus, to evaluate their applicability as chemical biomarkers. Chub mackerel were collected in the East China Sea, the Sea of Japan, and the Pacific Ocean, with body sizes ranging from 51 to 388 mm. The total fatty acid and lipid contents (mg g–1) increased with growth, and the percent composition of fatty acids and lipids changed drastically. The percentages of docosahexaenoic acid (%DHA), stearic acid (%Ste), and arachidonic acid (%ARA) decreased and the percentage of oleic acid (%Ole) increased when the body length (fork length, FL) was about 250 mm. The amounts of triacylglycerols (TAG) in fish in the East China Sea were lower than in the Sea of Japan and Pacific Ocean. The percentage of TAG drastically increased at around 250 mm FL, however, the phosphatidylcholines (PC) drastically decreased. The ontogenetic differences in the fatty acid and lipid composition might be influenced by metabolic events such as growth and reproduction. The geographical differences in chub mackerel can be distinguished by using stable isotope ratios, the ω3:ω6 fatty acid and DHA:EPA (eicosapentaenoic acid) ratios, and six main fatty acids. These chemical biomarkers could be available for understanding habitat and migration of chub mackerel.