Paddy fields are classified as wetland environments, and they comprise a freshwater ecosystem. They are ecologically important habitats and breeding grounds for many aquatic insects, amphibians, and reptiles. However, the paddy field ecosystem is constantly threatened by climate change and indiscriminate use of pesticides. The meta-barcode analysis of eDNA (environmental DNA) method is highly effective in accumulating information on many organisms that inhabit the paddy field ecosystem because it can explore organisms that are difficult to identify with traditional sampling methods. The eDNA method is very effective for accumulating information on many organisms in the rice field ecosystem. It can indirectly identify the existence of taxa no longer found in the target ecosystem due to behavioral characteristics like amphibia. In the metabarcoding results of this study, genes of more than five species of frogs were found, but it was impossible to confirm all frog taxa, frog's morphological pictures, and croak sounds. On the other hand, some frog taxa had been found only in the metabarcoding analysis. The eDNA of frogs found only in metabarcoding is estimated to have been introduced from nearby areas inhabited by frogs rather than the target region. Due to the powerful analytical resolution of eDNA metabarcoding, this eDNA-based paddy field search is expected to help investigate the biodiversity in agricultural ecosystems.