This a list of khans of the Yarkent Khanate (1514–1677).
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, it included Kashgar, Yarkand, Khotan, Uchturpan, Aksu and Kucha)-became dependency of Dzungar Khanate under Tsewang Rabtan (1697-1727), 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 exchange, Tsewang Rabtan appointed Khoja Daniyal in 1720 a ruler of Altishar with obligation to deliver tribute to Dzungar capital in Kainuk (near present day Ghulja in Ili River Valley ) annually in person. Next Dzungar Khan Galdan Tseren (1727-1745) confirmed rights of Khoja Daniyal, but increased tribute, as result taxes, collected by Kara Taghlik Khojas in Altishar in favor of Dzungar Khanate, reached 55% of income of peasants, artisans and traders in Altishar. Increased taxes were caused by growing military expenses of 100,000 Dzungar Army that was involved in military conflicts with all neighbors of Dzungar Khanate, including Russian troops in Siberia. In 1752 Altishar restored its independence after revolt against Dzungar Khanate under leadership of Kara Taghlik leader Khoja Yusup, son of Khoja Daniyal. Khoja Yusup took advantage from struggle for power between Dzungar princes after death of Galdan Tseren in 1745, when 2 of his sons, Ajan (1745-1749) and Lama Darji (1749-1752), were killed within 7 years after short khanships and 2 nephews, Dawachi (1752-1755) and Amursana (1755-1756), came into struggle for power after that. Khoja Yusup arrested all pro-Dzungar Beks in Altishar, expelled all Dzungars from the country and stopped tribute payments to Dzungar Khanate in 1752. In May 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 (which were sent here originally by the Qianlong Emperor on demand of Amursana, who asked the Manchu emperor to aid him to overthrow Dawachi from Dzungar Khanate's reign) and sent to Altishar to claim mandate of Qing China for the country. Burhan ad-Din Khoja sent letter with ultimatum of surrender to Kara Taghlik leader Khoja Jahan, the eldest son of Khoja Daniyal, who was declared a Khan of Altishar after death of Khoja Yusup in 1755. In his letter Burhan ad-Din Khoja claimed that he was appointed a ruler of Altishar by new Dzungar Khan Amursana ( old Dzungar Khan Dawachi fled to Uchturpan after losing battle to Qing troops in Baghistan (Ili River Valley) where he was captured with his son Lodja Noyon by Burhan ad-Din Khoja's people in July 1755, then handed over to Qing troops in Ili on August 1, 1755, Qings delivered him to Beijing for imprisonment on November 20, 1755) and Amursana in turn was appointed a Dzungar Khan by the Qianlong Emperor, so Khoja Jahan must return to Amursana all taxes that Kara Taghliks collected in Altishar for several years since 1752 and beg him for his life and lives of all relatives after that. Khoja Jahan burnt out letter of Burhan ad-Din Khoja after reading it to the people during military council in the royal palace Altunluk in Yarkand and declared a total war against Ak Taghliks. In ensuing bloody war Ak Taghlik brothers emerged victorious and established full control of Altishar in January 1756 but refused to submit to Qings after that. They killed Qing China emissary Amintu with 100 Manchu troops in Kucha on July 2, 1757, who was sent to Altishar to determine the sizes of tribute and taxes to be paid by each city monthly and annually to Qing China and also terms of sending of peasants (Taranchis) to Ili River Valley, where headquarters of Qing Army in occupied territory of New Line (Xinjiang ) were located, for cultivation of land and providing food for troops, the practice, that was previously employed by Dzungars since 1713. So, the war between Altishar and Qing China became imminent. In the end of 1759 Altishar was conquered by Qing China (with both Ak Taghlik Khojas having been killed on October 17, 1759 after fierce 2-years fighting with conquering Qing Army since spring 1758), 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 during military campaigns in 1756-1757 . It happened after last Dzungar Khan Amursana rebelled in October 1755 against Qing troops, which refused to leave occupied Ili River Valley, and massacred most of them, also he recognized that was deceived by the Qianlong Emperor and will never be let to rule the whole Dzungar Khanate and decided to oppose Qing plans to liquidate Dzungar Khanate with dividing Dzungaria into 4 administrative districts with separate Dzungar chieftains in each. In response, the Qianlong Emperor sent a 200,000-strong Qing army to Dzungaria in the spring of 1756 with order to quell rebellion by any means. Because resistance of Dzungars wasn't stopped and only increased, the Qianlong Emperor ordered to Military Council in Beijing on March 23, 1757 to take decisive actions against " Thieves and Criminals" and approved offer of Commander-in-chief of Qing Army in Dzungaria Zhao Hui to eliminate the whole Dzungar nation till last baby. Dzungaria was devastated during 1756-1758 with total loss of population up to 1,000 000 ( 40% of which fled, 30% were killed in actions and 30% died due to epidemic of smallpox, that started in 1757 and spread throughout all corners of Dzungaria ), completely depopulated and later colonized by migrants from different parts of China. Amursana fled to Russia where later he died due to illness, after that his dead body was handed over to Qings by Russian authorities.