In the mid-ninth century, these ancient Uighur people were finally conquered by Turkic Kirghiz in the mid-ninth century. The majority of the Uighurs, who were scattered over many areas, moved to the Western Region under the Anxi Governor's Office, and areas west of Yutian. Some went to the Tufan principality in western Gansu Province. The Uighurs who settled in the Western Region lived commingled with Turkic nomads in areas north of the Tianshan Mountains and western pasturelands as well as with Hans, who had emigrated there after the Western and Eastern Han dynasties. They intermarried with people in southern Xinjiang and Tibetan, Qidan (Khitan) and Mongol tribes, and evolved into the group now known as the Uygurs.

Between the ninth and the 12th centuries, the Uygurs made rapid socio-economic and cultural progress between the ninth and the 12th centuries. Nomadism gave way to settled farming. Commercial and trade ties with central China began to thrive better than ever before. Through markets, they exchanged horses, jade, frankincense and medicines for iron implements, tea, silk and money. With the feudal system further established, a land and animal owners' class came into being, comprising Uygur khans and Bokes (officials) at all levels. After Islam was introduced to Kaxgar in the late 10th century, it gradually extended its influence to Shache (Yarkant) and Yutian, and later in the 12th century to Kuya and Yanqi, where it replaced Shamanism, Manichae, Jingism (Nestorianism, introduced to China during the Tang Dynasty), Ao'ism (Mazdaism) and Buddhism, which had been popular for hundreds of years. Western Region culture developed quickly, with Uygur, Han, Sanskrit, Cuili and Poluomi languages, calendars and painting styles being used. Two major centers of Uygur culture and literature -- Turpan in the north and Kaxgar in the south -- came into being. The large number of government documents, religious books and folk stories of this period are important works for students of the Uygur history, language and culture.

In the early 13th century, Genghis Khan (1162-1227) appointed a senior official in the region. The Yuan Dynasty (1271-1368) established Bieshibali (present-day areas north of Jimsar) and Alimali (present-day Korgas) provinces. The Hami Military Command was set up during the Ming Dynasty (1368-1644). During the Qing Dynasty (1644-1911) the northern part of the Western Region, namely, north of Irtish River and Zaysan Lake, was under Zuo Fu General's Office in Wuliyasu. The General's Office in Ili exercised power over areas north and south of the Tianshan Mountains, east and south of Lake Balkhash and the Pamirs. Xinjiang was made a province in 1884, the 10th year of the reign of Emperor Guang Xu.

In the late 14th Century, the Uygur areas from Hami in the east to Hotan in the south were unified into a greater feudal separatist Kaxgar Khanate after more than two centuries of separatism and feuding from the late 14th century. As the capital was moved to Yarkant, it was also known as the Yarkant Khanate. Its rulers were still the offspring of Jagatai. During the early Qing period, the Khanate was a tributary of the imperial court and had commercial ties with central China. After periods of unsteady relations with the Ming Dynasty, the links between the Uygurs and ethnic groups in central China became stronger. Gerdan, chief of Dzungaria in northern Xinjiang, toppled the Yarkant Khanate in 1678 and ruled the Uygur area. The Qing army repelled in 1757 (the 22nd year of the reign of Emperor Qian Long) the separatist rebellion by the Dzungarian nobles instigated by the Russian Tsar, and in 1759 smashed the "Batu Khanate" founded by Poluonidu and Huojishan, the Senior and Junior Khawaja, in a separatist attempt.

In the Qing Dynasty(1644-1911), the Qing government introduced a system of local military command offices in Xinjiang. It appointed the General in Ili as the highest Western Regional Governor of administrative and military affairs over northern and southern Xinjiang and the parts of Central Asia under Qing influence and the Kazak and Blut (Kirgiz) tribes. For local government, a system of prefectures and counties was introduced.

The imperial court began to appoint and remove local officials rather than allowing them to pass on their titles to their children. This weakened to some degree the local feudal system. The court also encouraged the opening up of waste land by garrison troops and local peasants, the promotion of commerce and the reduction of taxation, which were important steps in the social development of Uygur areas.

Xinjiang was completely under Qing Dynasty rule after the mid-18th century. Although political reforms had limited the political and economic privileges of the feudal Bokes (lords), and taxation was slightly lower, the common ethnic people's living standards did not change significantly for the better. The Qing officials, through local Bokes, exacted taxes even on "garden trees." The Bokes expanded ownership on land and serfs, controlled water resources and manipulated food grain prices for profit.

In the Republic of China(1912-1949)
After foundation of the Republic of China in 1912, Xinjiang was a province under the China's central government.