We investigated the potential effect of sediment bypass tunnel that mitigate the ecological impact of dam reservoir on fragmented stream macroinvertebrate communities in Southeastern Swiss Alps. Using metabarcoding approach, we compared Bray-Curtis community's dissimilarities within rivers among 3 types of rivers: rivers fragmented by dams, rivers connected by sediment dam-bypass tunnel, and reference rivers (i.e. no dams).Among the three bypassed dams investigated, two showed significantly lower dissimilarities across the bypassed dams than non-bypassed dams, supporting the ecological mitigation effect of sediment bypass tunnel. However, one bypassed dam did not show a mitigation effect. This bypass has been operating only for 2 years, a period much shorter than the other two (=39 and 93 years), hence the elapsed time of bypass operation may not be enough to produce a mitigation effect. Overall, our metabarcoding approach allowed the rapid assessment of community structure of huge samples (i.e. 7369 individuals) collected from abroad for our research. Several technical limitations in the use of metabarcoding such as unsuccessful detection of rare taxa were also presented in this study.