Three species/subspecies of toads (Bufo japonicus japonicus, B. j. formosus, and B. torrenticola) show parapatric/sympatric patterns of distribution in Japan, and usually they are morphologically indistinguishable at early developmental stages. For quick and easy genetic identification of these three toads, we validated LAMP assay. We designed taxon-specific primers for LAMP assay on mitochondrial cytochrome b region, and these primer sets accurately assigned DNA samples derived from three toads to each taxon. Due to its instancy and simplicity, LAMP method could be a useful diagnostic tool to distinguish taxa which resemble each other.