Magnetic mapping is of increasing interest in studies of seafloor hydrothermal systems because such data can promote the understanding of the location and spatial extent of hydrothermal alteration zones. Previous studies reported both reduced and enhanced magnetization at hydrothermal fields of different tectonic settings, suggesting that the destruction and production of magnetic minerals are controlled by geological and tectonic background. In order to characterize magnetic response of arc-backarc hydrothermal systems, we investigated two hydrothermal fields of the southern Okinawa Trough. Near-seafloor vector magnetic measurements (altitude = ~80 m) were performed on the Irabu and Tarama hydrothermal fields using an underwater autonomous vehicle URASHIMA during the R/V Yokosuka cruise (YK14-16). The Irabu knoll is located on the axial area of backarc rift and consists of basaltic lavas. The Tarama knoll is located between backarc and arc along with dacite to rhyolite. The amplitude variation of observed near-seafloor magnetic anomaly is extraordinarily larger at the Irabu knoll (~12000 nT) than the Tarama knoll (~1000 nT). Sea-surface anomaly also shows larger amplitude variation at the Irabu knoll (~760 nT) than Tarama knoll (~460 nT). Rock magnetic analyses for collected samples revealed that the basaltic lavas in the Irabu knoll carry much higher natural remanent magnetization than rhyolitic lavas in the Tarama knoll. Therefore the difference of magnetic anomaly amplitude should be caused by the host rock variation. The distribution of crustal magnetization estimated from the magnetic anomaly obsercation revealed that the Irabu and Tarama hydrothermal fields are associated with reduced magnetization, as seen at some lava-hosted hydrothermal sites. These observations reflect locally altered up-flow zones formed due to hydrothermal activity, because hydrothermal alteration processes destroy iron-titanium oxide minerals (titanomagnetite), which carry magnetic remanence in oceanic basalts, and/or accumulate thick hydrothermal deposits with non-magnetic minerals. Comparisons with detailed bathymetry and magnetization distribution of the Irabu knoll displayed that the magnetization low were located along with the rim of cauldron structure, indicating that hydrothermal fluids through the alteration zone rise from the deep of the caldera fault.