Originally known as , it was part of the Kingdom of Chūzan during the Sanzan period. In 1416, the Aji of Yomitanzan Magiri, Gosamaru, helped Shō Hashi invade Hokuzan. Although Gosamaru lived in Yamada Castle, Shō Hashi allowed him to build Zakimi Castle. The castle, along with other castle sites in Okinawa, was designated a World Heritage Site by UNESCO in November 2000. The port of Hamanaga, which was located in the north of Yomitanzan, was an important center of Nanban, or "southern barbarian", trade of the Ryukyu Kingdom. Yomitanzan was also the site of a landing during the Invasion of Ryukyu by Satsuma Domain in 1609. After Japan annexed Ryukyu in 1879, Yomitanzan continued to be a magiri; all of the magiri were abolished in 1907 and Yomitanzan became a village.