Beginning in the mid-14th century a new khanate, in the form of a nomadic tribal confederacy headed by a member of the family of Chagatai, arose in the region of the Ili River.

Although the rulers enjoyed great wealth from trade with the Ming dynasty, it was beset by constant civil war and invasions by the Timurid Empire, which emerged from the western part of the erstwhile Chagatai Khanate.

The Moghul Khans considered themselves heir to Mongol traditions and called themselves Mongghul Uls, from which the Persian term "Moghulistan" comes.

Ming dynasty Mandarins called the Moghuls "the Mongol tribes in Beshbalik (Chinese: 别失八里; pinyin: Bié Shī Bā Lǐ)".

[6] Because of this, they were much more resistant to changing their way of life; they retained their primarily nomadic lifestyle for several centuries and were among the last of the Mongols who converted to Islam to do so.

It was bounded on the west by the province of Shash and the Karatau Mountains, while the southern area of Lake Balkhash marked the northern limit of Moghul influence.

Besides Moghulistan, Nanjiang, and Beijiang, several other regions were also temporarily subjected to Moghul rule at one time or another, such as Tashkent, Ferghana and parts of Badakhshan.

The Buddhist kingdom in Beijiang centered around Turfan was the only area where the people were identified as "Uyghurs" after the Islamic invasions.

After the Islamization of Turfan, the non-Islamic term "Uyghur" would disappear until the Chinese Nationalist leader Sheng Shicai, following the Soviet Union, introduced it for a different, Muslim population in 1934.

Moghulistan, which had formed the eastern portion of the Chagatai Khanate, became independent in 1347 under the Chagatayid named Tughlugh Timur.

[2] The eastern regions of the Chagatai Khanate in the early 14th century had been inhabited by a number of Mongol nomadic tribes.

[12] In the 1340s as a series of ephemeral khans struggled to hold power in Transoxiana, little attention was paid by the Chagatayids to the eastern regions.

[13] Tughlugh Timur (1347–1363) was thereby made the head of a tribal confederacy that governed the Tarim Basin and the steppe area of Moghulistan (named after the Moghuls).

Unlike the khans in the west, however, Tughlugh Timur was a strong ruler who converted to Islam (1354) and sought to reduce the power of the Dughlats.

[14] Tughlugh Timur converted to Islam, whose concepts of ummah, ghazat (holy war), and jihad inspired his territorial expansionism into Transoxiana.

In 1360 he took advantage of a breakdown of order in Transoxiana and his legitimacy as descendant of Chagatai Khan[15] to invade the region and take control of it, thereby temporarily reuniting the two khanates.

This takeover provoked a period of near-constant civil wars, because the tribal chiefs could not accept that Qamar-ud-Din, a "commoner", could accede to the throne.

[19] Those Mongols allied with the nomadic Buddhist, Christian and Shamanist rebels of the Issyk Kul and Isi areas against the Chagatai Khan Tarmashirin in the 1330s upon his conversion to Islam.

Moghul rule in the region was restored by Uwais Khan (1418–1428), a devout Muslim who was frequently at war with the Oirats (Western Mongols) who roamed in the area east of Lake Balkash.

When Esen Buqa died in 1462, the Dughlat amirs were divided over whether they should follow his son Dost Muhammad, who was then seventeen or his brother Yunus Khan.

[22] After the death of Dost Muhammad in 1469,[23] Yunus Khan reunited the khanate, defeated the Uzbeks and maintained good relations with the Kazakhs and Timurids, but the western Tarim Basin was lost to a revolt by the Dughlats.

Towards the end of Yunus' reign, his son Ahmad Alaq founded a breakaway eastern Khanate in greater Turpan.

In 1503 he traveled west to assist his brother Mahmud Khan (1487–1508), the ruler of western Moghulistan in Tashkent, against the Uzbeks under Muhammad Shaybani.

Ahmad Alaq died soon after and was succeeded by his son Mansur Khan (1503–1545), who captured Hami from Kara Del, a Mongol dependency of Ming China, in 1513.

Mahmud Khan spent several years trying to regain his authority in Moghulistan; he eventually gave up and submitted to Muhammad Shaybani, who executed him.

A nephew of the dead amir, Mirza Muhammad Haidar Dughlat fled to Mughal Empire in India and eventually conquered Kashmir, where he wrote a history of the Moghuls.

[33] In the late sixteenth and early seventeenth centuries, the Yarkent Khanate (1514–1705) underwent a period of decentralization, with numerous subkhanates springing up with centers at Kashgar, Yarkand, Aksu and Khotan.

[34] In 1677, Khoja Afaq of the Aq Taghlik fled to Tibet where he asked the 5th Dalai Lama for help to restore his power.