Mahmud Sultan (Qilich Khan) (born c. 1614; died 1636), the second son of Timur Sultan and the founder of Ishakiyya branch of Nakshbandi Khojagan Sufi Order. He died in the age of 22 when he was poisoned by Khoja Yahiya.
Sultan Ahmad Khan (Pulat Khan) (born c. 1613; died 1640), the ruler of the Yarkent Khanate from 1636 until 1638. He restored the khanship with help of Kara Taghlik leader Khoja Yahiya. He resigned in 1638 on demands of Kashgar and Yarkand emirs in favor of Abdullah Khan.
Nur ad-Din Sultan ( in Aksu 1649–1667) 1667–1668 in Kashgar and Yengisar, the youngest son of Abdullah Khan, died in 1668 in the age of 31 due to heavy drinking, reigned one year with help of the Kara Yanchuks , mercenaries from Dzungars and Kyrgyz tribes, who were first recruited on service in Yarkand Khanate during last years of reigning of Abdullah Khan.
Ismail Khan (in Chalish 1666–1669, in Aksu 1669–1670) 1669, the 5th son of Abduraim Khan, grandson of Abdurashid Khan, disciple of Kara Taghlik leader Khoja Ubaidullah (Khoja Shadi), son of Khoja Yahiya, was declared a Khan in Aksu after Abdullah Khan fled to India.
YuIbars Khan ( In Kashgar 1638–1667, since age of 8) 1669–1670, the eldest son of Abdullah Khan, disciple of Ak Taghlik leader Khoja Mohammad Yusuf (son of Khoja Kalon who died in 1598 and was founder of Ishkiya branch of Nakshbandi Khojagan Sufi Order, followers of which were known as Aktaghliks) and his son Appak Khoja, during his reign positions of Ak Taghliks in Yarkand Khanate greatly increased, was killed in 1670 by Dzungar supporter Erka Bek, main controller of Dzungar Khan Sengge (1653–1671) in Yarkand, in the age of 40.
Abd al Latif Sultan 1670, son of Yulbars Khan, who was set up on khanship by Ak Taghliks, was killed in the same 1670 by Kara Taghliks with all other sons of Yulbars Khan.
Ismail Khan 1670–1678, restored on April 2, 1670, by Kara Taghliks, expelled Appak Khoja and his son Yahia Khoja from the country in 1670, in 1678 was captured by Dzungars in Yarkand ( they were invited into the country by Ak Taghlik leader Appak Khoja who used for this recommendation letter from 5th Dalai Lama with whom he met in exile), died in Ili River Valley ( Baghistan) in 1680 in the age of 56.
Abd ar-Rashid Khan II 1678–1682, the eldest son of Sultan Said Baba Khan, set up on khanship by Dzungar Galdan (1671–1697), who came to Yarkand with Appak Khoja and was rewarded by him with 4,000 pcs of fine clothes and 100,000 silver coins (tangas) for military help. In 1682, Abd ar-Rashid Khan II was sent to Ili under escort by Dzungars, who reacted on complaint of Appak.Khoja to Galdan against Abd ar-Rashid Khan II and again were generously rewarded by him. Abd ar-Rashid Khan II fled to Beijing with his son Sultan and surrendered to the Kangxi Emperor in 1696 after Galdan's collapse.
Muhammad Imin Khan 1682–1692 (1680–1682 in Chalish, 1682 in Turfan), second son of Sultan Said Baba Khan. After his oldest brother Abd ar-Rashid Khan II was expelled, Muhammad Imin Khan was recalled from Turpan and elected a Khan on a Kurultai of Kashgar and Yarkand Begs. Organized several expeditions against Dzungars. It caused no objections from Appak Khoja, who even married Muhammad Imin Khan's sister Khanum Padshah to save his already shaken prestige and influence among population. In 1692 Muhammad Imin Khan issued State Order (Yarlik ) about expelling Appak Khoja and his son Yahiya Khoja from Yarkent Khanate. In response, Appak Khoja swore to exterminate all descendants of Chengiz Khan in the country and collected troops of his disciples. In decisive battle near Kargilik in 1692 most Muhammad Imin Khan's troops deserted him and joined Khojas. Muhammad Amin Khan fled to the mountains where he was killed.
Yahiya Khoja (in Kashgar 1690–1692) 1692–1695, son of Appak Khoja, set up on khanship by Appak Khoja, killed in 1695 by Hanim Padsha.
Hanim Padsha (Khanum Padshah) 1695, sister of Muhammad Imin Khan, widow of Appak Khoja, was killed in 1695.
Muhammad Mumin Khan (Akbash Khan) 1695–1705, the youngest son of Sultan Said Baba Khan, great-grandson of Abdurashid Khan, disciple of Kara Taghliks, recalled Kara Taghlik leader Khoja Daniyal (died in 1735) from exile in Kashmir to resist Ak Taghliks and Dzungars, fled to India in 1705 under protection of Aurangzeb of Moghul Empire.
Shah Khan 1543–1570, the eldest son of Mansur Khan
Koraish Sultan (Khotan 1533–1570; Chalish 1570–88) 1570–1588, son of Abdurashid Khan, expelled to India in 1588 by Abdul Karim Khan, where he was received by Moghul Emperor Akbar the Great, who gave him one of regions of India in suyurgal (inheritable possession of land with all peasants on it).
Muhammad Khan (in Kashgaria 1591–1610), 1588–1591, son of Abdurashid Khan
Abduraim Khan 1591–1594, 1605–1634, the youngest son of Abdurashid Khan, died in 1634 in the age of 77. Had 9 sons, eldest of them was Abdullah Khan.
Khudabende Sultan 1594–1605, son of Koraish Sultan, died in 1605
Muhammad Khashim Sultan (in Chalish) 1608–1610, son of Khudabende Sultan, grandson of Koraish Sultan, was killed in 1610 by Abduraim Khan in Kucha.
Abdullah Khan (in Chalish, in Kashgaria 1638–1669) 1634–1638, the eldest son of Abduraim Khan.
Abu'l Muhammad Khan 1638–1653, son of Abduraim Khan. In 1646 sent an embassy to Beijing to congratulate the newly proclaimed Manchu Shunzhi Emperor as first Emperor of the Qing dynasty of China, that succeeded the Ming dynasty, which was overthrown by Manchus in 1644. Embassy brought dozens of horses, camels and precision jade stones as a gift to the emperor. In accordance with ancient Chinese tradition it was declared as a Tribute from Vassal of China. In 1646 Turpan was granted by Qing China the rights to trade in the capital Beijing and in the city of Lanzhou, capital of Gansu province.
Sultan Said Baba Khan ( in Kumul 1636–1653) 1653, died in 1680 in the age of 53, 4th son of Abduraim Khan
Ibrahim Sultan ( in Khotan 1638–1653) 1653–1655, son of Abduraim Khan, was killed in 1655
Sultan Said Baba Khan (restored) 1655–1680. In 1656 sent an embassy to Qing China with gifts for the Shunzhi Emperor, who accepted them and issued an imperial order on October 19, 1656, concerning trade regulations with Turpan, and sent back with mission 338 pieces of silk garment and 723 rolls of fine silk as a gift to Turpan ruler.
Abd ar-Rashid Khan II (in Chalish 1678–1680) 1680–1682, the eldest son of Sultan Said Baba Khan, was captured in 1682 by Dzungars and held in captivity for 14 years, was rescued in 1696 by the Kangxi Emperor's Qing troops, who launched military operations against Dzungar Galdan Boshugtu Khan in Khalkha region and defeated him here in June 1696. Abdurashid Khan II was interrogated by Qings and gave them clues about Dzungar Khan's capture, explaining that he could to flee to Kukunor only through Turpan and Kumul, which supplied his troops with food. Qings contacted ruler of Kumul Ubaidullah Khan (?–1709), he captured son of Galdan Boshugtu Khan Tsewang Baljir, who came to Kumul for food, and handed over to Qings. Galdan Boshugtu Khan died of illness in 1697, his dead body was captured by Ubaidullah Khan as well and handed over to Qings. The Kangxi Emperor rewarded Abdurashid Khan II and Ubaidullah Khan for active participating in the operation for liquidating of Galdan Boshugtu Khan, Abdurashid Khan II was given permit to return to his homeland, while his son Sultan was retained in Beijing as actual hostage. Ubaidullah Khan was given the title of Jasak prince with his existing title of Tarkhan being confirmed (exemption from taxation and punishment until committing of 10th crime), the seal, imperial silk clothes and silver money, that was declared by Qings as incorporating of Kumul Khanate into Qing China. Son of Ubaidullah Khan Gapur Bek was appointed as assistant of Commander-in-chief of Qing troops in Suzhou, Gansu province, with permanent residence in this city that actually meant taking him as a hostage by Qings.
Muhammad Imin Khan 1682–1690, second son of Sultan Said Baba Khan, great-grandson of Abdurashid Khan. In 1682 sent an embassy to Qing China with gifts for the Kangxi Emperor. In his letter to the Kangxi Emperor, Muhammad Imin Khan apologized for delay of Tribute from Turpan, that was caused by recent turmoil in the country. The Kangxi Emperor accepted gifts and gave recommendation to replace horses for Jade in Tribute ( with compensation of 300 rolls of fine silk for 100 Tael (about 3.78 kg) of Jade). Embassy from Turpan was accompanied by Envoy from Kashgar Islam Khoja who informed the Kangxi Emperor of recent Dzungar invasion and asked some help against Galdan Boshugtu Khan, but result of negotiations is unknown
