Chagatai khans

The Chagatai Khans were the heads of the Chagatai Khanate from Chagatai Khan's inheritance of the state in 1227 to their removal from power by the Dzungars and their vassals in 1687. The power of the Chagatai Khans varied; from its beginning, the khanate was one of the weakest of the Mongol states, and often its rulers were merely figureheads for ambitious conquerors (see Kaidu and Timur).

Note: The following list is incomplete and, at times, possibly slightly inaccurate. It also excludes several collateral lines that ruled over minor territories and were relatively unimportant.

The remnants of the state fell to two different rival branches of Khojas- Ak Taghliks and Kara Taghliks. Aqtaghlyq branch of Khojas, a confederation under the influence of the Dzungars, took power in Kashgar where Ahmad Khoja, son of Yahiya Khoja, was declared a Khan. In Yarkand Kara Taghliks took power with Khoja Daniyal being declared a Khan, that caused civil war between Kashgar and Yarkand.
In 1713 remnant of Yarkant Khanate - Altishar ( union of 6 cities)-became dependency of Dzungar Khanate under Tsewang Rabtan, paying annual tribute from all 6 cities in amount of one silver tanga from soul, for Yarkand it was established in amount of 100,000 silver tangas, for Kashgar-67,000 silver tangas, this time Kara Taghliks were established by Dzungars to be responsible for collecting tribute. In 1752 Altishar restored its independence after revolt against Dzungar Khanate under leadership of Kara Taghlik leader Khoja Yusup, son of Khoja Daniyal. In 1755 sons of Ahmad Khoja and great grandsons of Appak Khoja, Ak Taghliks Burhan ad-Din Khoja and Jahan Khoja were rescued by Qings troops in Ili River Valley from Dzungar's captivity and sent to Altishar to claim mandate of Qing China for the country. In ensuing bloody war with Kara Taghliks brothers emerged victorious and established total control of Altishar in 1756 but refused to submit to Qings after that. In 1759 Altishar was conquered by Qing China, that created province Nanlu (Southern Road) on its territory in 1760, while province Beilu (Northern Road) was created on the territory of former Dzungar Khanate, that was exterminated by Qing China in 1756.

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Wikipedia