Two species of Japanese toads, Bufo japonicus formosus and Bufo torrenticola, were identified in a mountain stream using random amplified polymorphic DNA (RAPD) and mitochondrial (mt) DNA sequencing techniques. We detected RAPD fragments and mtDNA sequences specific for each species collected from allopatric areas. These molecular data indicated that most of the toads collected from their sympatric areas in a mountain stream in central Japan were backcross hybrids to B. torrenticola, even though they possessed the mtDNA of B. j. formosus. Directional introgression probably occurred between the males of B. torrenticola and females possessing the mtDNA of B. j. formosus, resulting from B. j. formosus being compelled to spawn in stream side pools, especially during the initial period of contact between the two species. Furthermore, most of the hybrid individuals probably backcrossed to the numerically predominant B. torrenticola. Such conditions might have resulted from recent and continuous flooding which created changes in the topography of the Bufo spawning habitat.