At its height in the late 13th century the khanate extended from the Amu Darya south of the Aral Sea to the Altai Mountains in the border of modern-day Mongolia and China, roughly corresponding to the area once ruled by the Qara Khitai (Western Liao dynasty).

[16] For example, Giovanni de' Marignolli, who visited Yuan dynasty in the 1340s, referred to Almaliq (the capital of the Chagatai Khanate) as "Almalek of the Middle Empire (Imperium Medium)".

[18] Matsui Dai introduced the expression "[missing] -dadu mongγo[l] u(l)us" in a Uighur script document excavated from Turfan, and based on the example of "Middle Empire (Imperium Medium)," argued that this should be read as "Dumdadu Mongγol Ulus".

Matsui proposed that "it seems probable that Dua or his descendants took the brand-new official state name Dumdadu Mongol Ulus in order to affirm that their polity was renewed, as did the emperor Qubilai, who in 1271 adopted the official state name Dai Ön Yeke Mongol Ulus.

[22] Alghu rebelled against Ariq Böke upon securing power and defected to Kublai Khan's side in the Toluid Civil War.

[27] In September 1298, Duwa captured Temür Khan's son-in-law, Korguz, and put him to death, but immediately after that suffered a disastrous defeat by Yuan forces.

One of Buqa Temür's brothers, Taliqu, seized power, but Duwa's family rebelled and killed him at a banquet.

Another kuriltai was held in the Chagatai Khanate, which elected another of Duwa's sons, Esen Buqa I, who took the throne ceded by Kebek.

In 1315, Esen Buqa invaded the Ilkhanate in support of Duwa's grandson, Dawud Khoja, who had set himself up in eastern Afghanistan.

He defeated an Ilkhanate army on the Murgab and reached as far as Herat, but was forced to retreat when the Yuan dynasty attacked him from the east.

[31] Giovanni de' Marignolli, a papal legate, arrived in the Ili valley the following year on his way to the Yuan dynasty.

He built a church and baptized some people during his stay, and the presence of Christianity lasted until the end of the Mongol era.

[37] In the east, the powerful Dughlats enthroned a son of Esen Buqa I, Tughlugh Timur as khan of Moghulistan in 1347.

He then besieged Samarkand but suffered harsh attrition due to an epidemic so that by the next year he was forced to retreat from Transoxania.

Under Esen Buqa II, the powerful Dughlat Sayyid Ali, who had helped him to the throne, became very influential and held both Kucha and Kashgar.

[47] The Timurid ruler Abu Sa'id Mirza schemed to split the Moghuls in two, so he summoned Yunus in 1456 and supported his authority in the Ili region.

Yunus also took advantage of political infighting in the west to vassalize Umar Shaikh Mirza II's realm in Fergana.

In 1487, Mahmud gave refuge to Muhammad Shaybani, who then seized Bukhara and Samarkand from the Timurids in 1500, making himself ruler of Transoxania.

Muhammad immediately turned against Mahmud, who called his brother Ahmad Alaq for help, and defeated both the Moghul khans and took them prisoner.

Abdurashid spent his reign fighting the Kyrgyz people and the Kazakhs, who made incursions on the Ili region and Issyk Kul.

Abdul was succeeded in 1590 by his brother Muhammad Sultan, who repelled an invasion by the Khanate of Bukhara under Abdullah Khan II.

Ismail reversed the power struggle between the two Muslim factions and drove out the Aq Taghliq leader, Afaq Khoja.

Afaq fled to Tibet, where the 5th Dalai Lama aided him in enlisting the help of Galdan Boshugtu Khan, ruler of the Dzungar Khanate.

The new khan forced Afaq Khoja to flee again, but Abd ar-Rashid's reign was also ended unceremoniously two years later when riots erupted in Yarkand.

Afaq's son Yahiya Khoja was enthroned but his reign was cut short in 1695 when both he and his father were killed while suppressing local rebellions.

The Dzungars installed a non-Chagatayid ruler Mirza Alim Shah Beg, thereby ending the rule of Chagatai khans forever.

[54] Ahmad Alaq's reduced nomadic realm (known as the Turpan Khanate) came into frequent conflict with the Oirats, Kyrgyz people, and Kazakhs.

Šamba received support from the Ming dynasty, which closed its borders to Turpan and expelled its traders from their markets, which eventually forced Ahmad to give up his ambitions in Hami due to unrest in his realm.

In 1514, Mansur's brother Sultan Said Khan captured Kashgar, Yarkand, and Khotan from Abu Bakr and forced him to flee to Ladakh.

[59][60] The Chagatai Mongols remained mostly nomadic in their mode of government and did not settle down in urban centers until the late 15th century.