After his father’s fiasco in the war with Oyrat Mongols, Yolebars Sultan began to interfere with the state affairs. On his side was the Hoja of the Aktaglik Sect, who harbored discontent against the khan. When Abdul Rahman Khan started to quell, once again, his challenging children, Yolebars Sultan sided with Oyrat Mongols and, with the latter’s support, fought back and took Kashgar. The father, Abdul Rahman, who found everyone turning away from him, had no other option but to give up the khanship and leave in the guise of paying pilgrimage to Mecca. Both Yolebars Sultan and Ismail Khan, who took the khanship shortly after, seized power through the support of a certain faction within Oyrat Mongol. After taking control, they started to murder dissident kinsmen and suppress opposite Islamic sects. The Karataglik Sect was the first to be quelled; and the Aktaglik Sect was the next, after Ismail Khan got in power. Amidst the political and religious conflicts, Apak Hoja of the Aktaglik Sect went to Tibet and secured the involvement of Dalai Lama. Thus Gal dan from the Junggar division of the Oyrat Mongols sent troops in 1680 (the 19th year of Kangxi reign of Qing Dynasty) and captured Yarkand City. So the Yarkand Khanate was extinguished and Junggar’s comprehensive rule over both the north and south of the Tianshan Mountains began.
Since the west expeditions of Chinggis Khan, the most profound impact of the Mongols’ rule on the Western Regions was that the Golden Clan of Chinggis Khan was regarded as local orthodox royal blood. This idea was especially evident in the period of Eastern and Western Chagatai Khanates and Yarkand Khanate after the Mongol Yuan Dynasty. No matter how powerful Imis could be, they still had to find a descendant of the Golden Clan, or even make up one, and let him be the khan. It is highly possible that it is due to this orthodox idea that most of the Turkic-speaking tribes previously active in different ways in the time of the Turki Khanate, Karakhanid Dynasty in particular, could no longer be found in later historical records. If we call such development “Mongolization” of the Western Regions, then the “Turkic-ization” of the many Mongol tribes was equally evident. In the several centuries when they ruled the Western Regions, the Mongol tribes gradually lost their own language and adopted local Turkic language as they lived, mixed and fought with the natives. Today, the records about the Eastern and Western Chagatai Khanates and Yarkand Khanate were mostly written in the local Turkic language.
The second biggest influence of the Mongol rule over the Western Regions was the destruction of local economy and society by the conflicts and wars between members of the ruling class in the later stage of the Mongol Yuan Dynasty, particularly during the Eastern and Western Chinesische mauer peking Chagatai Khanates and Yarkand Khanate periods. Prolonged wars were not only capable of destroying property and life and consuming resources, but also likely to turn into irreversible destruction since the Western Regions was extremely vulnerable ecologically. This might be an important factor explaining the long-term economic backwardness in that area afterwards.