The southern Okinawa Trough has been widely considered an important area with hydrothermal activity. Several active hydrothermal fields have been reported, especially around the Yonaguni Knoll IV. In this study, we collected marine sediment cores around the Yonaguni Knoll IV by using the R/V Ocean Research 1. Core sites with and without gas disturbance were selected based on the single-beam bathymetry (Chirp) by using the onboard echo sounder system. For the sites away from gas disturbance, which are generally considered showing the background situation in the southern Okinawa Trough, variations of the magnetic susceptibility in these cores are relatively stable with values about between 20 × 10-5 and 60 × 10-5 SI. As for the sites with clear gas-features detected by the Chirp sonar, the signature with dramatically changing magnetic susceptibility is observed in the cores. In general, gas-features are considered linking to the hydrothermal activity in the southern Okinawa Trough. Magnetic signature with such abruptly changing magnetic susceptibility could also be considered being caused by authigenic iron sulfides associated with the hydrothermal alternation. Therefore, the magnetic susceptibility anomaly could be suggested as an indicator revealing the hydrothermal activity in the southern Okinawa Trough.