The Amago clan were a branch of the Kyōgoku clan based in Izumo Province. In the latter part of the fifteenth century, Amago Tsunehisa, the deputy military governor of Izumo, refused to pay taxes demanded by the Muromachi bakufu. In 1484, Kyōgoku Masatsune, the military governor, then removed Tsunehisa from his role as and drove him out of Gassantoda Castle. Enya Kamon-no-suke was dispatched to Gassantoda as the newly appointed deputy military governor, but, in 1486, Tsunehisa launched a sudden attack and recaptured the castle. In the absence of a military governor, he asserted control over Izumo in lieu of the Kyōgoku, and the Amago clan became the sengoku daimyō of Izumo.
In 1508, Ōuchi Yoshioki traveled to Kyōto with forces from the Sanyō, Sanin, and Kyūshū regions and supported Ashikaga Yoshitada to return for a second term as shōgun. Hosokawa Takakuni acted in concert with the march to Kyōto. Tsunehisa followed along and joined the Battle of Funaokayama. As a sign of appreciation to Yoshioki and Takakuni, Amago Tsunehisa conferred one of the characters from Takakuni’s name upon his second son, Amago Kunihisa, and one of the characters from Yoshiaki’s name upon his third son, Enya Okihisa.
In 1518, Tsunehisa’s eldest son, Amago Masahisa, died in battle. In 1530, his third son, Okihisa, conspired with influential kokujin, or provincial landowners, from Bingo Province and the western and southern portions of Izumo Province to revolt against Tsunehisa. This resulted in a series of fateful events including the loss of lives. Thereafter, until 1539, Tsunehisa maintained an apparent peace with the Ōuchi and expanded his domain to the east. Despite originating from a branch of the clan, Tsunehisa rose from the role of a deputy military governor to a daimyō, developing an iron works in Izumo, promoting marine trade, and expanding his territory in the Sanin Region.
In 1537, Tsunehisa conveyed control of the clan to his grandson, Amago Haruhisa. During his time as head of the clan, Haruhisa served as the shugo for the eight provinces in the Sanin and Sanyō regions (Izumo, Oki, Hōki, Inaba, Mimasaka, Bizen, Bitchū, and Bingo) and attained a role as an official, known as a shōbanshū, of the Muromachi bakufu.
During the Tenmon period (1532-55), the Amago pacified most of Bitchū and aimed to expand their influence from Bizen to Mimasaka and Harima. In 1539, Haruhisa set his sights on marching to Kyōto, but the encirclement by the Ōuchi collapsed and pressure from the west increased, so he withdrew his forces to Izumo.
In 1540, a total of 30,000 troops invaded Aki Province to attack the Mōri, a powerful kokujin allied with the Ōuchi, at their home base of Yoshida-Kōriyama Castle. The Mōri protected the castle with support from Ōuchi Yoshitaka and Sue Harukata, and the invaders withdrew in 1541 from the Siege of Yoshida-Kōriyama Castle.
In 1542, Ōuchi Yoshitaka, in the role of commanding general, assembled 20,000 troops including the Mōri and kokujin from Aki, Suō, and Iwami provinces, to enter Izumo. This expedition lasted for one year and four months in the Siege of Gassantoda Castle, but guerilla attacks on the supply lines and defenses stretching deep into the heart of Amago territory took their toll, causing kokujin including Mitoya Hisasuke, Mizawa Tamekiyo, Honjō Tsunemitsu, and Kikkawa Okitsune to betray the Ōuchi and join the Amago. After the loss of key figures in battle such as Ōuchi Harumochi and Kobayakawa Masahiro, the weakened army fled in 1543, drawing to a close this First Battle of Gassantoda Castle.
In 1554, as successor to the Amago territory, Haruhisa aimed to consolidate his power in Izumo by eliminating the group of elite fighters that exercised control over territory, known as shingūtō, led by Amago Kunihisa (the second son of Tsunehisa) and his eldest son, Amago Sanehisa. In addition, he sought to expand his domain. The Amago clan reached their peak in 1555 when, based in Izumo Province, their hegemony extended to Hōki, Oki, the eastern portion of Iwami, Mimasaka, the northern portion of Bingo, the northwest portion of Bitchū, the western portion of Bizen. The Amago name was also known to the Muromachi bakufu based in Kyōto.
In 1559, the Mōri commenced an attack against the Amago in the northern portion of Bingo Province. Haruhisa dispatched forces from the eastern portion of Mimasaka to Bingo, but those kokujin aligned with the Amago were expelled from the northern portions of Bingo, and, having no other options, the Amago forces retreated from Bingo. This resulted in a loss of control over territory in the southern portion of Bingo province from Shōbara. The Yamana clan captured more territory following an attack against kokujin in the western portion of Inaba Province. The Amago relinquished control over the northern portion of Bitchū after Mimura Iechika and kokujin in Bitchū aligned with the Mōri assaulted Matsuyama Castle.
Mōri Motonari brought order to confusion in the wake of an internal struggle within the Ōuchi clan, becoming a sengoku daimyō with a domain extending from Aki to Suō and Nagato provinces. In 1557, he invaded the eastern portion of Iwami. Haruhisa prevailed in an ensuing battle around a mountain with a contested silver mine known as Iwami Ginzan, but suddenly died in 1560.
After succeeding Haruhisa, his eldest son, Amago Yoshihisa, engaged the shōgun, Ashikaga Yoshiteru, in an effort to reconcile with the Mōri. Although the combatants reached an initial agreement, Mōri Motonari unilaterally disregarded the deal and, in 1562, launched a full-blown attack in Izumo in the Second Battle of Gassantoda Castle. Yoshihisa took refuge in the castle while the Mōri struck the ten supporting castles known as the Amago jikki which formed a line of defense for the Amago in Izumo. In 1563, Motonari attacked Shiraga Castle, laid siege to Gassantoda, and initiated a plan to cut-off provisions to the castle. Motonari also applied artifice by defaming a senior retainer named Uyama Hisakane who had earlier contributed his personal resources to procure provisions for the defenders. The ever-suspicious Yoshihisa responded by purging Hisakane. He finally had no choice other than to surrender the castle in 1566, bringing to an end the rule of the Amago clan as sengoku daimyō.
Afterwards, surviving retainers, including Yamanaka Yukimori and Tachihara Hisatsuna, served Amago Katsuhisa, and, with the support of Oda Nobunaga, led the resistance, temporarily gaining control of a castle in an attempt to revive the Amago. However, in 1578, Katsuhisa took his own life after the Mōri captured Kōzuki Castle in Harima, and Yukimori was executed, resulting in the final demise of the Amago clan.