The Yamashita-cho anthropological site is in a cave in the Naha limestone, the oldest member of the Pleistocene Ryukyu limestone. The Naha limestone is forming the high level terrace of the area and cut by step faults with the NW-SE direction.
After the deposition of the Naha limestone, the southern part of the Okinawa Island upheaved domically, when antithetic faults and step faults occurred in the area. The formation of the Yamashitacho cave might be closely related to the crustal movement.