This paper reports a series of studies leading to the discovery of a submarine hydrothermal field (called Nakayama Field) at an arc seamount (12°43′N, 143°32′E) in the southernmost part of the Mariana Trough, western Pacific Ocean. We first detected hydrothermal plumes characterized by water column anomalies of temperature, light transmission, Mn, Fe, Al, O2, CH4, and δ13C of CH4 above the summit caldera of the seamount. Then deep-tow camera surveys confirmed the existence of hydrothermal activity inside the caldera, and an ROV dive finally discovered white smoker-type fluid venting associated with vent fauna. A high concentration of aluminum in the plume and white smoker-type emissions imply acidic hydrothermal activity similar to that observed at the DESMOS Caldera in the eastern Manus Basin, Papua New Guinea. Anomalously low δ13C (CH4) of −38‰ of a vent fluid sample compared to other arc hydrothermal systems along the Izu-Bonin and Mariana Arcs suggests an incorporation of biogenic methane based on a subsurface microbial ecosystem.