Stock discrimination study for juvenile ayu, Plecoglossus altivelis altivelis from stomach of Japanese seabass, Lateolabrax japonicus in the Nuta River estuary was conducted using prey otolith morphology and Sr/Ca profiling. Out of 7 individuals, 3 individuals identified as hatchery-stock ayu that had crystallized otolith. Based on the Sr/Ca profiling for 4 individuals that have normal otolith, 1 individual was identified as an amohidromous form and 3 individuals were identified as hatchery-stock ayu. The results showed that otolith-based approches could provide insight into stock discrimination for even highly digested ayu that have lost all phenotypic characteristics.