There is a strong possibility that the lower part of Yabiji was dry land during the Last Glacial Period.

In particular, during the period from spring to summer when the tidal range is large, there are some reefs that appear on the sea surface like islands, leading to Yabiji sometimes being called the "Phantom Continent.

[12] Each year on March 3 of the lunar calendar (around the beginning of April in the Gregorian calendar), when the largest annual tidal difference takes place in Yabiji, a traditional event known in the Miyako Islands as Sanitsu (サニツ), meaning "going down the beach," takes place in which women gather to drive off bad luck and ward off evil spirits.

[15][16][17] On May 16, 1797, the British Royal Navy sloop-of-war HMS Providence was surveying East Asia under the command of William Robert Broughton when she ran aground on a coral reef at the northwestern tip of Yabiji,[18] flooded from the bottom, and sank.

"[19][20][21] While cruising in the waters of the Miyako Islands on June 7, 1902, the Imperial Japanese Navy destroyer Shinonome ran aground in Yabiji.

In 1983, the Miyako Ferry company and the Hayate Company began holding tours of Yabiji in conjunction with the annual Yabiji Festival in which their ferries landed tourists on the reefs that emerged above the sea surface during low tides for several days before and after Sanitsu (March 3 on the lunar calendar, around the beginning of April in the Gregorian calendar).

[2] In 2008, a diving survey conducted by the Okinawa Prefectural Buried Cultural Properties Center found the remains of a foreign ship, believed to be HMS Providence.

[19][20][21] On August 1, 2008, the Geospatial Information Authority of Japan published a re-edited version of the 1:25,000 topographic map of Yabiji that included Fudeiwa (フデ岩), or Fude Rock.

[24] On March 27, 2013, the Government of Japan′s Agency for Cultural Affairs recognized Yabiji as a place of great importance — an "excellent coastal scenic landscape that has been enjoyed for its connection with Miyakojima's unique lifestyle culture" and "the largest coral reef group in Japan" — and designated it as a Place of Scenic Beauty (名勝; meishō) and a Natural Monument (記念物, kinenbutsu) of Japan.

With the opening of the Irabu Ohashi Bridge between Miyako Island and Irabu Island in January 2015, both Miyako Ferries and Hayate discontinued their operation of regular ferry service between Hirara Port in Miyakojima on Miyako Island and Sarahama Port on Irabu and sold their ferries, bringing the landing tours to an end before the low-tide season of 2015.

[30] Between 2008 and 2018, the living part of the reef decreased by an estimated 70% due to coral bleaching resulting from rising water temperatures in Yabiji.