Whale carcasses support unique biological assemblages in deep sea. The carcasses release reducing chemicals such as hydrogen sulfide and nourish chemosynthesis-based biological communities. Two “stepping-stone” hypotheses regarding whale-fall ecosystems have been proposed. One explains a dispersal pathway for hydrothermal vent/hydrocarbon seep faunae in the deep sea and another an evolutionary process of vent/seep specialists. Here we summarize the whale-fall ecosystems, especially in Japanese waters and our attempts to verify the hypotheses.