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Environmental DNA (eDNA) has recently been used for detecting the distribution of macroorganisms in various aquatic habitats. In this study, we applied an eDNA method to estimate the distribution of the Japanese clawed salamander,  Onychodactylus japonicus , in headwater streams. Additionally, we compared the detection of eDNA and hand-capturing methods used for determining the distribution of  O .  japonicus . For eDNA detection, we designed a qPCR primer/probe set for  O .  japonicus  using the 12S rRNA region. We detected the eDNA of  O .  japonicus  at all sites (with the exception of one), where we also observed them by hand-capturing. Additionally, we detected eDNA at two sites where we were unable to observe individuals using the hand-capturing method. Moreover, we found that eDNA concentrations and detection rates of the two water sampling areas (stream surface and under stones) were not significantly different, although the eDNA concentration in the water under stones was more varied than that on the surface. We, therefore, conclude that eDNA methods could be used to determine the distribution of macroorganisms inhabiting headwater systems by using samples collected from the surface of the water.

Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods