To identify the origin of various fishes and reconstruct their migration history at the individual level, isotope analysis is a powerful alternative to artificial tagging. We used a novel individual-based methodology to reconstruct individual migratory and/or trophic shifts associated with growth based on isotopic data in the vertebral centrum of adult Japanese flounder Paralichthys olivaceus in Sendai Bay. We measured carbon and nitrogen isotope ratios (δ¹³C and δ¹⁵N) in muscle tissues, and conducted a segmental isotope analysis of bulk δ¹³C (δ¹³C_bulk), bulk δ¹⁵N (δ¹⁵N_bulk), and δ¹⁵N of glutamic acid (δ¹⁵N_Glu) and phenylalanine (δ¹⁵N_Phe) in vertebral collagen. The δ¹⁵N_Glu and δ¹⁵N_Phe values for bone collagen revealed an increase in trophic position and a shift to lower trophic baselines (δ¹⁵N_Base: indicative of δ¹⁵N values of primary trophic sources) for most individuals. For both δ¹³C_bulk and δ¹⁵N_bulk, we detected significant positive correlations between values for muscle and the outermost section of vertebral collagen. A nonlinear time-series analysis of δ¹³C_bulk and δ¹⁵N_bulk suggested that a combination of intrinsic (the timing of migration from the nursery to deep offshore areas in juveniles) and extrinsic (habitat and/or food qualities) factors influence the isotopic chronology. A segmental isotope analysis revealed the segregation of individuals among sampling sites at all life stages and changes in trophic positions and δ¹⁵N_Base values during growth. Our results suggest that the P. olivaceus population in Sendai Bay has both temporal and spatial structure. The temporal structure may be caused by variation in the timing of migration from the nursery to the deep offshore area in juveniles, and the spatial structure may be explained by individual variation in habitat preferences.