In the coastal marine fish Apogon notatus most individuals emigrate from the neritic breeding ground in winter and return there in the following spring (migratory type), while some indi- viduals reside in the neritic habitat throughout the year (resident type). In the present study, we con- ducted carbon and nitrogen stable isotope analysis to estimate their winter migration routes and to elucidate the underlying spatial heterogeneity in the food web structure of the coastal ecosystem, and compared the results with those of A. semilineatus, a deepwater congener. A. notatus fed on a vari- ety of zooplankton and zoobenthos in the neritic habitat, whereas A. semilineatus fed on pelagic mysids exclusively. The former showed more enriched δ 13 C than did the latter, indicating strong reliance on benthic production. Such a difference in stable isotope ratio was attributed to spatial heterogeneity in the coastal food web structure: benthic microalgal production predominates in the neritic food web, while the pelagic deepwater food web is characterized by phytoplankton produc- tion. After returning from winter migration, A. notatus showed marked depletion of δ 13 C compared to its non-migratory counterpart residing in the neritic habitat. Thereafter, the migratory type showed enrichment of δ 13 C during its stay in the neritic breeding ground, approaching that of the resident type. The results suggest that most A. notatus migrated to the deepwater habitat and spent a couple of winter months there. Stable isotope analysis revealed that life history polymorphism (i.e. migratory and resident types) exists in the A. notatus population.