We conducted a self-potential survey at an active hydrothermal field, the Izena hole in the mid-Okinawa Trough, southern Japan. This field is known to contain Kuroko-type massive sulphide deposits. This survey measured the self-potential continuously in ambient seawater using a deep-tow array, which comprises an electrode array with a 30-m-long elastic rod and a stand-alone data acquisition unit. We observed negative self-potential signals not only above active hydrothermal vents and visible sulphide mounds but also above the flat seafloor without such structures. Some signals were detectable >50 m above the seafloor. Analysis of the acquired data revealed these signals' source as below the seafloor, which suggests that the self-potential method can detect hydrothermal ore deposits effectively. The self-potential survey, an easily performed method for initial surveys, can identify individual sulphide deposits from a vast hydrothermal area.