Seafloor hydrothermal system and deep subsurface are of great interest for microbiologists as paradise of unusual lives so-called “Extremophiles” in this planet. Such peculiar microorganisms have been believed to be minority in the earth throughout the long history after the early evolution of life. Recent investigations for microorganisms present in the active hydrothermal seafloor and subsurface have revolutionized the concept. Ubiquity, predominance and diversity of extremophiles in the present and past global environments signify the unresolved, but significant role in the co-evolution of earth and life. In this article, we summarize the expeditions for the microbial world in the seafloor hydrothermal system and deep subsurface and shed light on the foci of the future investigation.