Estimating the migration pathway of chub mackerel using a state-space model with nitrogen isoscapes and compound-specific nitrogen isotope analysis

• Time profiles of baseline nitrogen isotope ratio (δ 15 N Base ) of chub mackerel were reconstructed from layered eye lens. • A state-space model assimilating phytoplankton δ 15 N isoscapes (δ 15 N Phy ) with eye-lens δ 15 N Base via an isotope observation equation was developed. • Two individuals hatched off Choshi migrated east along the Kuroshio Extension and then north; one individual followed a more northerly route via the Oyashio region • Reconstructed trajectories were validated against sea-surface temperature histories. • Ocean-current forcing was necessary for plausible routes: the current-informed model outperformed the no-current model. Changes in marine environments, driven by climate change and fishing pressure, have altered the migratory patterns of migratory fish. The Pacific stock of chub mackerel shows large variability in biomass yet changes in key early-life migration routes remain unclear. Here, we present an iso -logging state-space framework for migratory fish that assimilates isotopic time series archived in fish tissues, monthly isoscapes with ocean-current data. We measured bulk δ 15 N values across 34 eye lens layers for one individual and in 33 layers for two individuals of the Pacific stock of chub mackerel ( Scomber japonicus ) (δ 15 N Eye ). From the δ 15 N Eye , corrected using the δ 15 N of glutamic acid and phenylalanine, we derived δ 15 N Base , the δ 15 N value at the base of the food web, and compared it with seasonally varying phytoplankton isoscapes (δ 15 N Phy ). Assuming active swimming on the ocean current field, we developed a state-space model that incorporates both advection and active movement and reconstructed the continuous migration pathways from hatch to six months post-hatching. This framework successfully reconstructed continuous migration pathways and inferred hatch locations primarily off Choshi (140–144°E, 35–37°N). The estimated trajectories were consistent with the known thermal habitat of chub mackerel and previously reported regional migration patterns. By integrating eye lens isotopic proxies with oceanographic constraints, this method fills observational gaps left by tag-based techniques and is particularly effective for larval and juvenile stages. This framework is widely applicable to other marine organisms and to other tracers.