In this research project, I promote research for the application of environmental DNA to investigate rare or introduced varieties. In particular, I have focused on the development of estimating biomass by environmental DNA concentration in reservoirs and streams, the estimation of the exotic varieties’ distribution and biomass, application of environmental DNA technique on introduced or rare water plants. In study A, I measured biomass at the whole reservoir by collection when the reservoir is fully dehydrated and compared the biomass and environmental DNA amount. As a result, there are explicit correlation between eDNA amount and biomass, and its behaviour was not related to where samples were collected such as shore or buffer. In study B, I have done the development of real-time PCR primer probe and outdoor investigation on Hydrilla verticillate of and Egeria densa which are submerged plants of Hydrocharitaceae to confirm usefulness of eDNA analysis as aquatic plant distribution estimation method. As consequence, it was found that there is a correlation between biomass and eDNA amount and there are more plant eDNAs in some particles where animal eDNAs aren’t. The eDNA technique developed in this study is expected to be an effective mean to estimate biomass in various species, investigate organism distribution, determine the invasion scale of exotic genotype quickly.