A new hydrothermal vent site in the Southern Mariana Trough has been discovered using acoustic and magnetic surveys conducted by the Japan Agency for Marine-Earth Science and Technology's (JAMSTEC) autonomous underwater vehicle (AUV), Urashima. The high-resolution magnetic survey, part of a near-bottom geophysical mapping around a previously known hydrothermal vent site, the Pika site, during the YK09-08 cruise in June–July 2009, found that a clear magnetization low extends ∼500m north from the Pika site. Acoustic signals, suggesting hydrothermal plumes, and 10m-scale chimney-like topographic highs were detected within this low magnetization zone by a 120kHz side-scan sonar and a 400kHz multibeam echo sounder. In order to confirm the seafloor sources of the geophysical signals, seafloor observations were carried out using the deep-sea manned submersible Shinkai 6500 during the YK 10-10 cruise in August 2010. This discovered a new hydrothermal vent site (12°55.30′N, 143°38.89′E; at a depth of 2922m), which we have named the Urashima site. This hydrothermal vent site covers an area of approximately 300m×300m and consists of black and clear smoker chimneys, brownish-colored shimmering chimneys, and inactive chimneys. All of the fluids sampled from the Urashima and Pika sites have chlorinity greater than local ambient seawater, suggesting subseafloor phase separation or leaching from rocks in the hydrothermal reaction zone. End-member compositions of the Urashima and Pika fluids suggest that fluids from two different sources feed the two sites, even though they are located on the same knoll and separated by only ∼500m. We demonstrate that investigations on hydrothermal vent sites located in close proximity to one another can provide important insights into subseafloor hydrothermal fluid flow, and also that, while such hydrothermal sites are difficult to detect by conventional plume survey methods, high-resolution underwater geophysical surveys provide an effective means.