Recently, there has been an increasing recognition that population and life history diversity within individual species can contribute to their stability and robustness. For example, in regional populations with multiple habitats, if some habitats exhibit less productivity in a given year, other habitats may compensate for this, thereby mitigating the annual variability of productivity across the region. Therefore, comprehending the utilization of habitats by a population is crucial for ensuring the persistence of the targeted population. The strontium isotope ratio (87Sr/86Sr) in otoliths is a reliable tracer to estimate fish life history because stream-specific Sr isotope ratios are seasonally stable. In this study, we used isotopic analysis to assess the life history diversity of an endangered salmonid fish in order to estimate its resilience. Firstly, we collected water from 108 points along the Nagara river in Gifu Prefecture, Japan. And then, we measured 87Sr/86Sr ratio in each river water using an MC-ICP-MS to constrict 87Sr/86Sr isoscape. Secondly, a total of 103 samples of Oncorhynchus masou masou were collected from Nagara River and extracted otolith to estimate the river of origin and life history of this species. And then, we measured 87Sr/86Sr ratios along a core-to-edge otolith transect using an MC-ICP-MS with a laser ablation-desolvating nebulizer dual sample intake system. Our results indicate that O. masou was produced in several watersheds, and the natal habitat of O. masou in each of these watersheds fluctuates annually. Furthermore, our results also suggest that there is significant variability in the timing of migration to the sea among individuals within the population. These results suggest a need for the management of multiple watersheds to enhance the sustainability of the salmonid population. Additional analysis is expected to contribute to the development of effective resource management strategies.