In 1999, a marine seismic structure survey was conducted in the northernmost Okinawa Trough. Outcrops of the acoustic basement through the sedimentary layers are seen in the obtained structures. Velocities of lower layer in upper crust are varying laterally from 5.7 to 6.2 km/s and thickness of 6.0-km/s layer ranges from 3 to 9 km. The lower crust has uniform thickness of about 15 km. The Pn velocity is 7.7-7.8 km/s and the total crustal thickness is about 25 km including sedimentary layers. The structure is in a first approximation similar to that of island arcs. However, the large heterogeneity of upper crust can be interpreted as a result of crustal thinning. The low Pn velocity and the outcrops of the acoustic basement relate to igneous activity in this area. These results suggest that the northernmost part of the Okinawa Trough is in the incipient stage of a back arc rifting.