The southern part of the Itoigawa-Shizuoka Tectonic Line represents the boundary between the rapidly uplifting Akaishi range and the Kofu basin. The tectonic relation between the different parts of the fault system and the surrounding geological units is yet to be fully explained. In order to reveal seismic activity that might be related to the southern segments of the fault system, a seismic array observation was conducted in the autumn of 2005. The arrival times of 434 local earthquakes, two vibroseis shots and eleven explosive shots were used in a joint inversion to determine earthquake locations and a 3-D velocity structure of the crust. The relocated events are in good correlation with the estimated deeper extension of the active faults in the area. The seismic velocity model jointly obtained coincides with the geological structure in the area of study. In particular, a thick moderately low V p zone was found beneath the Akaishi range and a high velocity zone beneath the Kofu basin. The moderately low velocity was attributed to the relatively young sedimentary rocks that form the accretionary prism units of the SW Japan arc and the high velocity to the older igneous rocks constituting the Izu-Bonin arc crust.