The caves were first excavated in 1887 by Tsuboi Shōgorō, a professor at Tokyo Imperial University and one of the pioneers of Japanese archaeology and anthropology.
Tsuboi found Jōmon period pottery fragments at the site as well, and postulated that the caves were originally dwellings for a race of people smaller than the modern Japanese, possibly the Koro-pok-guru people of Ainu legend, and were later converted into tombs by the invading Yamato peoples.
However, his theory was challenged after further research in the 1920s, notably by Mitsutarō Shirai and other archaeologists, who argued that the structure of the caves and artifacts recovered were consistent with other late Kofun period tombs, and that there was no material evidence to indicate that the Koro-pok-guru were anything more than a folktale.
As the largest grave cluster in Japan and was designated as a National Historic Monument on March 7, 1923.

Despite the protected status, about one tenth of the site was destroyed during the final days of World War II, when some of the caves were enlarged in order to create an underground aircraft engine factory for Nakajima Aircraft Company by some 3,000-3,500 conscripted and volunteer laborers.
The war ended before the factory came into operation.

The site is partially open to the public and contains two museums.
One is the Yoshimi Town Archaeological Museum, which displays some of the artifacts discovered as well as other items from the surrounding area.
The other is a local history museum with a diorama of Sengoku period Matsuyama Castle, which formerly existed on the summit of a nearby hill.
The caves were first excavated in 1887 by Tsuboi Shōgorō, a professor at Tokyo Imperial University and one of the pioneers of Japanese archaeology and anthropology. Tsuboi found Jōmon period pottery fragments at the site as well, and postulated that the caves were originally dwellings for a race of people smaller than the modern Japanese, possibly the Koro-pok-guru people of Ainu legend, and were later converted into tombs by the invading Yamato peoples. However, his theory was challenged after further research in the 1920s, notably by Mitsutarō Shirai and other archaeologists, who argued that the structure of the caves and artifacts recovered were consistent with other late Kofun period tombs, and that there was no material evidence to indicate that the Koro-pok-guru were anything more than a folktale. As the largest grave cluster in Japan and was designated as a National Historic Monument on March 7, 1923.
Despite the protected status, about one tenth of the site was destroyed during the final days of World War II, when some of the caves were enlarged in order to create an underground aircraft engine factory for Nakajima Aircraft Company by some 3,000-3,500 conscripted and volunteer laborers. The war ended before the factory came into operation.
The site is partially open to the public and contains two museums. One is the Yoshimi Town Archaeological Museum, which displays some of the artifacts discovered as well as other items from the surrounding area. The other is a local history museum with a diorama of Sengoku period Matsuyama Castle, which formerly existed on the summit of a nearby hill.
Yoshimi Hundred Caves