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In this study, to discuss on the applicability of eDNA as a new method to investigate fish diversity at streams, we applied eDNA at 4 streams (Geum River, Ji Stream, Hwangji Stream, Seomjin River), where endangered species are inhabits, with conventional survey (cast net and kick net). The average (±standard deviation) number of species investigated by eDNA were 19 species (±4.4), and it was relatively higher than average of conventional survey, 10 species (±4.8). Most of case, in this study, eDNA was more efficient than conventional survey. However, there were errors on species identification of Korean endemic species and aliied species from eDNA, and it seems the universal primer (MiFish primer set) is not suitable for them. Furthermore, some of endangered species, caught by conventional method, was not detected by eDNA. As the present universal primer is not suitable for identify the every freshwater fish species in Korea, the complementing or development of universal primer is needed, and the eDNA application after species specific marker development for detecting specific species like endangered species should be considered. In conclusion, if the manual for field survey method by eDNA is developed, we expect applicability enlargement for water ecosystem survey.