A new hydrothermal vent site in the southern Mariana Trough has been discovered using acoustic and magnetic surveys. Two stage surveys by the autonomous underwater vehicle (AUV) Urashima (Japan Agency for Marine-Earth Science and Technology, JAMSTEC) and the manned submersible Shinkai 6500 (JAMSTEC) were conducted in 2009 and 2010, respectively. In the first stage, we detected a clear magnetization low that extends from a previously known hydrothermal vent site, the Pika site, by using a vector magnetometer attached to the AUV. The acoustic signals suggest the presence of hydrothermal plumes emanating from the seafloor within the water column of the 120kHz side scan sonogram; 10 m scale chimney like structures in the 400-kHz multibeam bathymetry data were also detected in the area of low magnetization. These observations strongly suggest the presence of an unseen hydrothermal vent. The subsequent submersible dive discovered a new vent site, which was named the Urashima site . The calculated absolute magnetization using the submersible-attached magnetometer succeeded in estimating the extent of hydrothermally altered zone for both the Pika and Urashima sites. It should be emphasized that the search for a hydrothermal vent site was a direct consequence of the geophysical surveys undertaken in the first stage. Our method can bridge the gap between conventional hydrothermal plume surveys (resolution on a scale of 103 m) and visual/photographic surveys (resolution on a scale of 100 m) and can precisely delineate the hydrothermally altered zone.