The stable carbon and nitrogen isotopes and fatty acid composition oftapertail anchovy (Coilia mystus) at four migration stagescollected around the Changjiang Estuary were analysed to investigate thevariations in the trophic biomarkers during the fish migration. δ13 C and δ15N values of C. mystusranged from −21.5 to −15.4‰ and from 6.9–15.8‰, respectively. Both δ13C and δ15N were enriched during migration.Polyunsaturated fatty acids were the dominant fatty acids and the majorfatty acids found in C. mystus wereC20:5n-3, C22:6n-3, C20:4n-6, C16:0, C18:0, C16:1n-7, C18:1(n-9, n-7) and C20:1 + C22:1.Significant changes among C. mystus at different migrationstages were found both in the fatty acid composition and specific fatty acidconcentration. Though the enrichment of stable isotopes may due to multiplefactors (e.g. diet shift, environment and ontogeny), the dietary influencecan be determined by the variation in fatty acid composition. Changes in theconcentrations of benthic markers (C18:1n-7 and C20:4n-6) and pelagic markers (C18:1n-9and C20:1 + C22:1) in C. mystus during the migration maysuggest that benthic and pelagic food sources alternately dominated theanchovies' diet during different migration stages. It seems that applicationof multiple biomarkers in the trophic study of migratory fish will elevatethe reliability of the analysis.