Migration, an important aspect of many species, consists of time and spatial aspects. Recently, novel techniques such as use of stable isotope clocks (SIC) and eDNA (DNA fragments in environment) have been proposed as alternatives to traditional methods of studying fish migration. This study investigated the applicability of SIC analysis, which takes advantage of different rates of change in isotope ratios of species’ tissues after a diet-switch, in estimating time since migration, and eDNA analysis in determining the distribution of Hasu fish -during its reproductive-migration to L. Biwa tributaries. Water samples including fish counts and environmental parameters for eDNA analysis and specimen for SIC were collected monthly from selected tributaries. δ¹³C isotope ratios from muscle and mucous tissues were obtained using IR-Mass Spectrophotometry. qPCR analysis was used to detect and quantify Hasu eDNA from water samples. Hasu eDNA was detected in some sites where fish were observed and in other sites where fish were not observed. A mismatch between some qPCR and field results was also observed -highlighting one challenge facing eDNA analysis. Time estimates from SIC increased as reproductive season progressed (range: 21-71days). SIC also revealed variation in migration time between individuals at each sampling -which is novel information.