Form Mongol Empire to Khanate of Yarkand
As Kara-Khitan Khanate and Western Xia perished, the Uyghurs were to be subordinated as Mongol Empire. People in Western Regions including Uyghurs were called 'coloured eyes people' and granted position following Mongolians. Uyghurs used their experience and knowledge to the full extent as they were called the 'Teacher of Mongolian Administration' and became the intellect of Mongolia. During Chagatai Khanate time, they gained a fame as Uyghur merchants by traveling all around the world and getting engaged with trade.
Though Mongl Empire would be disrupted later, the area including East and West Turkistan was succeeded by Chagatai Khanate. Majority of people in western Chagatai Khanate were the nomadic Mongolians who settled in the city. They started calling themselves Chagatai while the Turkification of the language and acceptance of Islam progressed. On the oher hand, the people in the praire of eastern Chagatai Khanate who preserved pure nomadic and traditional Mongolian life called themselves Moghul (Mongol). In 1340, Chagatai Khanate disrupted in east and west holding the the Pamir mountain as a border after going through the disruptive inclination and befuddlement.
Tughlugh Timur, the Khan of East Chagatai Khanate (Moghulistan) integrated East Turkistan and in 1360, though it was temporal, he integrated the Chagatai Khanate. However it was defeated by the Timur that established Timurid Dynasty in West Chagatai Khanate and it was subordinated to West Chagatai Khanate. Though Moghulistan was subordinated to Timurid Dynasty, it preserved the power on the east half of Tian Shan South Course. This was the time that Islamicism in Tarim Basin was completed.
In 1500, Timurid Dynasty perished. Around the same time in East Turkistan, the territory of Moghulistan gradually shifted southward. In reign of Mansur, northern area of Tian Shan North Course was almost abandoned and it became the nomadic area by Kazakhs and Kyrgyz. In 1514, Said, the younger brother of Mansur seized Kashgar and established Khanate of Yarkand (Khanate of Kashgar). Later on, Khanate of Yarkand governed all the Tarim Basin and its dominance lasted until 1679.
In addition, the ethnic distribution this time, north for nomadic and south for fixated, is taken over until now.
The nominal sovereign of Khanate of Yarkand that governed Tarim basin was the Moghulistan family, the descendants of Chagatai, but the real sovereign was in the hand of the Islamic nobles, Khoja. Khoja are persons calls themselves descendants of Muhammad. However Khoja was facing the conflict with Ishaqis (Black Mountaineers) based on Yarkand and Afaqis (White Mountaineers) based on Kashgar over 'light of God'.
