The Yonaguni Knoll IV hydrothermal vent field (24°51′N, 122°42′E) is located at water depths of 1370–1385 m near the western edge of the southern Okinawa Trough. During the YK03–05 and YK04–05 expeditions using the submersible Shinkai 6500, both hydrothermal precipitates (sulfide/sulfate/carbonate) and high temperature fluids (Tmax = 328°C) presently venting from chimney-mound structures were extensively sampled. The collected venting fluids had a wide range of chemistry (Cl concentration 376–635 mmol kg−1), which is considered as evidence for sub-seafloor phase separation. While the Cl-enriched smoky black fluids were venting from two adjacent chimney-mound structures in the hydrothermal center, the clear transparent fluids sometimes containing CO2 droplet were found in the peripheral area of the field. This distribution pattern could be explained by migration of the vapor-rich hydrothermal fluid within a porous sediment layer after the sub-seafloor phase separation. The collected hydrothermal precipitates demonstrated a diverse range of mineralization, which can be classified into five groups: (i) anhydrite-rich chimneys, immature precipitates including sulfide disseminations in anhydrite; (ii) massive Zn-Pb-Cu sulfides, consisting of sphalerite, wurtzite, galena, chalcopyrite, pyrite, and marcasite; (iii) Ba-As chimneys, composed of barite with sulfide disseminations, sometimes associated with realgar and orpiment overgrowth; (iv) Mn-rich chimneys, consisting of carbonates (calcite and magnesite) and sulfides (sphalerite, galena, chalcopyrite, alabandite, and minor amount of tennantite and enargite); and (v) pavement, silicified sediment including abundant native sulfur or barite. Sulfide/sulfate mineralization (groups i–iii) was found in the chimney–mound structure associated with vapor-loss (Cl-enriched) fluid venting. In contrast, the sulfide/carbonate mineralization (group iv) was specifically found in the chimneys where vapor-rich (Cl-depleted) fluid venting is expected, and the pavement (group v) was associated with diffusive venting from the seafloor sediment. This correspondence strongly suggests that the subseafloor phase separation plays an important role in the diverse range of mineralization in the Yonaguni IV field. The observed sulfide mineral assemblage was consistent with the sulfur fugacity calculated from the FeS content in sphalerite/wurtzite and the fluid temperature for each site, which suggests that the shift of the sulfur fugacity due to participation of volatile species during phase separation is an important factor to induce diverse mineralization. In contrast, carbonate mineralization is attributed to the significant mixing of vapor-rich hydrothermal fluid and seawater. A submarine hydrothermal system within a back-arc basin in the continental margin may be considered as developed in a geologic setting favorable to a diverse range of mineralization, where relatively shallow water depth induces sub-seafloor phase separation of hydrothermal fluid, and sediment accumulation could enhance migration of the vapor-rich hydrothermal fluid.