Dzungar conquest of Altishahr

[2] The Naqshbandi Sufi Khojas, descendants of the Prophet Muhammad, had replaced the Chagatayid Khans as the ruling authority of the Tarim Basin in the early 17th century.

Khoja Afaq asked the 5th Dalai Lama when he fled to Lhasa to help his Afaqi faction take control of the Tarim Basin (Kashgaria).

[3] The Dzungar leader Galdan was then asked by the Dalai Lama to restore Khoja Afaq as ruler of Kashgaria.

His nephew and successor, Tse Wang Rabdan, ruled from Hami on the east to Khokand on the west, and, until his murder in 1727, was the most powerful of Zungarian rulers.

Sir Henry Howorth gives an interesting account of the relations between Tse Wang and the Russians, from which it appears that Peter the Great, attracted by rumours of gold in Eastern Turkestan, despatched a body of 3000 men up the Irtish with Yarkand as their objective; but the Zungars assailed the column and forced it to retire.

To return to the Khoja family, its most celebrated member was Hidayat Ulla, known as Hazrat Apak or "His Highness the Presence," head of the Ak Taulins, who was regarded as a Prophet second only to Mohamed.

Expelled from Kashgar he took refuge at Lhassa, where the Dalai Lama befriended him and advised him to seek the aid of the Zungars.

In 1678 the latter seized Kashgar, which remained in their power for many years, and Hazrat Apak ruled as the deputy of the Khan, paying tribute equivalent to £62,000 per annum.

Qing China received tribute from Muhammad Amin via Turfan two times, in 1690s the Mughals received an embassy from him, and in 1691 Muhammad Amin asked for deliverance from the "Qirghiz infidels" (Dzungars) when the Khan Subhān Quli of Bukhara received his embassy, these were attempts by Muhammad Amin to ask these foreign countries (Qing China, Mughal India, and Bukhara) for assistance against the Dzungars to regain independence.

[16] The Uighurs were forced with multiple taxes by the Dzungars which were burdensome and set by a determined amount, and which they did not even have the ability to pay.

Gold necklaces, diamonds, pearls, and precious stones from India were extracted from the Uighurs under Dāniyāl Khoja by Tsewang Rabtan when his daughter was getting married.

Trade, milling, and distilling taxes, corvée labor, saffron, cotton, and grain were also extracted by the Dzungars from the Tarim Basin.

Uighurs like Emin Khoja, 'ʿAbdu l-Mu'min and Yūsuf Beg supported the Qing attack against Dawachi, the Dzungar Khan.

[26] The Uch-Turfan Uighur Beg Khojis (Huojisi) supported the Qing General Ban-di against in tricking Davachi and taking him prisoner.

During this time, the Dzungar pioneered the local manifestation of the ‘Military Revolution’ in Central Eurasia after perfecting a process of manufacturing indigenously created gunpowder weapons.

Additionally, the Dzungar managed to enact an empire-wide system of laws and policies to boost the use of the Oirat language in the region.