Offshore northern Ishigaki-Jima Island, in the southern Okinawa Trough, offers outstanding opportunities to explore the rifting stage of a backarc system. We report the results of integrated marine geological and geophysical surveys with high-density survey lines in this area. We identify a graben bounded by normal faults and extending approximately 59 km in an ENE-WSW direction off-axis of the southern Okinawa Trough. Submarine volcanoes with active hydrothermalism and associated intrusive structures lie in the graben. Magnetic anomaly and seismicity data in and around the graben suggest the presence of relatively shallow magma acting as a heat source. All features identified in and around the graben suggest active rifting in the southern Okinawa Trough.