Yamato Japan and the Gaya Confederacy, which were located directly across the Korea Strait from one another, had very close diplomatic and commercial ties since prehistory until the conquest of Gaya by Silla in 562 AD.

Until recently Japanese historians had believed that Gaya, once called Mimana in Japanese, was controlled by Japan for most of its existence as an overseas colonial possession. Though this theory has been largely refuted since the 1970s, it remains a sensitive and re-occurring issue in modern-day Korea–Japan relations. In 2010, a joint study group of historians sponsored by the governments of Japan and South Korea agreed that Gaya had never been militarily colonized by ancient Japan.Yukiko Ishikawa and Masahiko Takekoshi, "History gap still hard to bridge", Yomiuri Shimbun, 25 March 2010.

Gaya and Japan Around 300 BC the introduction into Japan of agriculture and metallurgy from the regions of Korea which would later become Gaya helped bring a transition from the hunter-gatherer Jōmon culture into the Yayoi culture,Kenneth B. Lee, Korea and East Asia: The Story of a Phoenix (Westport, Connecticut: Praeger, 1997), 23–25.Song-Nai Rhee et al., "Korean Contributions to Agriculture, Technology, and State Formation in Japan", Asian Perspectives, Fall 2007, 417–422. though it is unclear whether this transition occurred due to a large-scale or small-scale invasion by a mainland Asian group or by the adoption of imports by the native inhabitants of the Japanese islands.Jared Diamond, "Japanese Roots", Discover Magazine, June 1998. As the nations of Yayoi Japan gradually unified, Gaya was the first foreign country with which they established relationsYoung-sik Lee, "Recent Research Trends on the History of Gaya in Korea", International Journal of Korean History, December 2000, 10–11. and by the beginning of the Kofun period around 250 AD Gaya remained the country with which Japan had the closest links.Tadashi Nishitani, "The Gaya Tumuli: Window on the Past", The Japan Foundation Newsletter, November 1993, 6.Kim Tae-sik, "Gaya Kingdom's Rightful Place in Korean History," Koreana, Spring 2006.Shin Kyung Choel, "Relations Between Gaya and Wa in the Third to Fourth Centuries AD", Journal of East Asian Archaeology, 2000, 112. Many Japanese archaeological sites dating from the Yayoi and the subsequent Kofun period testify to these contacts, with one holding artifacts that were 70% of Gayan origin.

Commerce and migration A thriving bilateral trade existed between Gaya and Japan. Gaya exported pottery, horse tack, and most crucially, iron and iron products, to Japan,Keith Pratt and Richard Rutt, Korea: A Historical and Cultural Dictionary (Richmond, London: Curzon, 1999), 205.William Wayne Farris, Sacred Texts and Buried Treasures: Issues in the Historical Archaeology of Ancient Japan (Honolulu: University of Hawaii Press, 1998), 72–73, 78, 84, 122.Song-Nai Rhee, "Gaya: Korea's Lost Kingdom", Korean Culture, Fall 1999, 8–10. and among the items Japan sent back to Gaya were bronze implements and jade magatama produced at Itoigawa.Shin Kyung Choel, "Relations Between Gaya and Wa in the Third to Fourth Centuries AD," Journal of East Asian Archaeology, 2000, 118. For most of its existence Gaya enjoyed a monopoly on major trade routes both between Japan and China and between Japan and the rest of Korea, and was thus an important intermediary between Japan and other Asian countries.Song-Nai Rhee, "Gaya: Korea's Lost Kingdom", Korean Culture, Fall 1999, 6.William Wayne Farris, Sacred Texts and Buried Treasures: Issues in the Historical Archaeology of Ancient Japan (Honolulu: University of Hawaii Press, 1998), 107.

Due to its proximity to China the Gaya Confederacy was also politically and technologically ahead of Japan and played an important role in Japan's development as a nation.Ch'on Kwan-u, "A New Interpretation of the Problems of Mimana", Korea Journal, February 1974, 11. Mass migrations of Gayans to Japan, often to escape strife between Gaya and neighboring Korean states, allowed Japan to produce on its own some of the products it had previously needed to import. Japan's sue pottery stylePaul Bahn, The Penguin Archaeology Guide (New York: Penguin Putnam, 2001), 427–428. and its first iron production were founded by Gayan immigrants, and Gayan warriors and officials were widely employed by the Japanese government.Song-Nai Rhee, "Gaya: Korea's Lost Kingdom", Korean Culture, Fall 1999, 12.Song-Nai Rhee et al., "Korean Contributions to Agriculture, Technology, and State Formation in Japan", Asian Perspectives, Fall 2007, 436–441.

Military alliance In 399 AD Japan formed a military alliance with Gaya and Baekje in opposition to the growing power of Goguryeo and Silla and from then on the Japanese often dispatched military forces to protect Gaya's territorial integrity, possibly in exchange for iron or other goods.Song-Nai Rhee et al., "Korean Contributions to Agriculture, Technology, and State Formation in Japan", Asian Perspectives, Fall 2007, 436.William Wayne Farris, Sacred Texts and Buried Treasures: Issues in the Historical Archaeology of Ancient Japan (Honolulu: University of Hawaii Press, 1998), 109–110. The defeat of one such Japanese expedition to Gaya is described on the Gwanggaeto Stele constructed in 414 AD.William Wayne Farris, Sacred Texts and Buried Treasures: Issues in the Historical Archaeology of Ancient Japan (Honolulu: University of Hawaii Press, 1998), 114–115. Japanese mercenaries were also allowed to serve in Korea, and the characteristically Japanese keyhole-shaped burial mounds which started to appear in Gaya and Paekche at the end of the 5th century are believed to be the tombs of those who died in Korea."倭の軍 - 朝鮮側の要請か", Yomiuri Shimbun, 12 January 2011. While the unity of the Gaya Confederacy was falling apart under pressure from neighboring states, one of the Gayan states, Ara Gaya, even formed a joint military mission with Japan in 540 AD which was staffed by Japanese officers.

In 554 AD Japanese soldiers fought alongside the armies of Gaya and Paekche at the Battle of Kwansan Fortress. The defeat of this alliance by Silla sealed the fate of Gaya which was conquered by Silla in 562 AD. By this time Paekche had already broken Gaya's monopoly on trade with Japan and would replace Gaya as Japan's most important conduit for foreign trade and mainland Asian culture.Jinwung Kim, A History of Korea: From Land of the Morning Calm to States in Conflict (Bloomington: Indiana University Press, 2012), 74.

"Mimana" historical debate The Nihon Shoki, an ancient text of Japanese history, states that Empress Jingū led a military expedition on the Korean peninsula which defeated the forces of Gaya, Paekche, and Silla, and made Gaya, which was referred to as Mimana,Ch'on Kwan-u, "A New Interpretation of the Problems of Mimana", Korea Journal, February 1974, 15, 17.Wontack Hong, Ancient Korea-Japan Relations: Paekche and the Origin of the Yamato Dynasty (Seoul: Kudara International, 2010), 143. into a colony under the control of a Japanese administrative office called "Mimana Nihon Fu".William Wayne Farris, Sacred Texts and Buried Treasures: Issues in the Historical Archaeology of Ancient Japan (Honolulu: University of Hawaii Press, 1998), 57–64. By the calculation of Japanese historians, it was said that this event took place in either 249 AD or 369 AD, and that Japan's domination of Mimana lasted until 562 AD.Ch'on Kwan-u, "A New Interpretation of the Problems of Mimana", Korea Journal, February 1974, 10. Though scholars had doubts about some aspects of this story, it was accepted as historical fact in both Japan and in Western countries that Japan had indeed possessed a colony called Mimana on the Korea peninsula between these dates.James H. Grayson, "Mimana, A Problem in Korean Historiography", Korea Journal, August 1977, 65, 67–68. This theory was particularly popular in Japan prior to and during Japan's occupation of Korea from 1910 to 1945 and was used as a justification for it. However, the theory continued to be supported well after 1945, including in the works of such influential Western Japanologists as George Sansom, John Whitney Hall, and Edwin Reischauer.George Sansom, Japan: A Short Cultural History (Englewood Cliffs, New Jersey: Prentice-Hall, 1962), 33–35.John Whitney Hall, Japan from Prehistory to Modern Times (New York: Delacorte Press, 1970), 37–43.Edwin Reischauer and John K. Fairbank, East Asia: The Great Tradition (Boston: Houghton Mifflin, 1958), 468–469.

Apart from the Nihon Shoki, evidence which was cited at the time to prove Japan's conquest of Gaya/Mimana included the exhuming of contemporary Japanese weaponry and armor from archeological sites in Korea, the inscription on the Gwanggaeto Stele which indicates that Japanese forces were occupying Gaya,William Wayne Farris, Sacred Texts and Buried Treasures: Issues in the Historical Archaeology of Ancient Japan (Honolulu: University of Hawaii Press, 1998), 60–61, 64–65, 116–117. and the titles received by Japanese monarchs from China's Liu Song dynasty acknowledging Japan's control over southern Korea. Today however, Japanese artifacts in Korea are seen as evidence of Japanese armies and mercenaries dispatched at the request of Gaya and Paekche, the inscription on the Gwanggaeto Stele is regarded as an exaggeration to justify Kokuryo's attacks,Pankaj N. Mohan, "Rescuing a Stone from Nationalism: A Fresh Perspective on the King Kwanggaet'o Stele of Koguryŏ," Journal of Inner and East Asian Studies, Summer 2004, 106–108. and the titles granted by China are considered to be most likely purely symbolic.Ch'on Kwan-u, "A New Interpretation of the Problems of Mimana", Korea Journal, February 1974, 19, 21–22. Historians have also called into question the historical reliability of the Nihon Shoki's account of events, as Japan was far behind Gaya technologically and still politically fractious at the time when Empress Jingu was alleged to have successfully invaded Korea.Song-Nai Rhee et al., "Korean Contributions to Agriculture, Technology, and State Formation in Japan", Asian Perspectives, Fall 2007, 447.Shin Kyung Choel, "Relations Between Gaya and Wa in the Third to Fourth Centuries AD", Journal of East Asian Archaeology, 2000, 120.William Wayne Farris, Sacred Texts and Buried Treasures: Issues in the Historical Archaeology of Ancient Japan (Honolulu: University of Hawaii Press, 1998), 106, 121.

In 1963 North Korean historian Kim Sŏk-hyŏng became the first scholar to call into question the existence of a Japanese colony in ancient South Korea. He instead put forward the so-called "branch kingdom theory", stating that "Mimana" was not in Korea at all but was a settlement of Gayan immigrants on the Japanese mainland in modern-day Okayama Prefecture which was eventually absorbed into Yamato Japan.William Wayne Farris, Sacred Texts and Buried Treasures: Issues in the Historical Archaeology of Ancient Japan (Honolulu: University of Hawaii Press, 1998), 65–66. Though Kim's theory is today not widely accepted outside of North Korea, it did spur other historians to pursue further research in this field.Young-sik Lee, "Recent Research Trends on the History of Gaya in Korea", International Journal of Korean History, December 2000, 9–10, 12–14. Hideo Inoue, the first Japanese historian to propose an alternative to the Japanese colonial theory, argued in a 1972 book that Mimana was actually a small self-governing settlement of Japanese immigrants living in Korea, though this idea is likewise not widely supported among academics.

The theory which is today dominant among both Korean and Japanese historians is the "diplomatic delegation theory", originally put forward by Masayuki Ukeda in 1974, which proposes that "Mimana Nihon Fu" as described in the Nihon Shoki was actually a sort of Japanese embassy handling diplomatic relations between the independent states of Gaya and Japan.