In order to obtain basic information for the implication of environmental DNA (eDNA) analysis into the National census on river environment in Japan (NCRE), the eDNA metabarcoding of fish was conducted in conjunction with the fish survey in NCRE. The survey was carried out in 48 habitats (pools, riffles etc.) in 15 study areas of 4 rivers. Environmental DNA analysis was less consistent with fish surveys at the habitat scale (50～100m scale), but was highly consistent (>70% on average) with fish surveys at the study area scale (～1 km section) and riverwide. It is considered that eDNA analysis using water samples from several habitat categories then evaluating it at the scale of the study area would detect more than 70% of the species caught in the fish survey. In addition, eDNA analysis using samples from the bottom layer could detect benthic fish that may leak out of the sampling of surface water alone.
