This is a list of Chagatai khans, who reigned as monarchs 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. It excludes several collateral lines that ruled over minor territories and were relatively unimportant.

Khans of the Chagatai Khanate Personal Name Reign Religion Chagatai Khan 1226–1242 CE Tengrism Qara Hülëgü 1242–1246 CE 1st ReignTengrism Yesü Möngke 1246–1252 CE Tengrism Qara Hülëgü 1252 CE 2nd Reign Tengrism Mubarak Shah His mother Orqina Khatun was regent during this time1252–1260 CE 1st Reign Islam Alghu bin Baidar 1260–1266 CETengrism Mubarak Shah 1266 CE 2nd Reign Islam Ghiyas-ud-din Baraq 1266–1270 CE Islam Kaidu bin Kashin and his son Chapar bin Kaidu ruled as de facto Khans from 1270 until 1304. The Chagatai Khans during this period were appointed by them but still rebelled when they tried to exert their authority. Negübei Under Kaidu bin Kashin 1270–1272 CETengrism Buqa Temür Under Kaidu bin Kashin 127?–1282 CETengrism Duwa Under Kaidu bin Kashin & Chapar bin Kaidu1282–1306 CETengrism Restoration of Chagatai Khanate independence. Duwa 1306–1307 CETengrism Könchek 1307–1308 CETengrism Taliqu 1308–1309 CE Islam Kebek 1309–1310 CE 1st ReignTengrism Esen Buqa I 1310–1318 CETengrism Kebek 1318–1325 CE 2nd ReignTengrism Eljigidey 1325–1329 CE Tengrism Duwa Temür 1329–1330 CETengrism Ala-ad-din Tarmashirin 1331–1334 CE Islam Buzan 1334–1335 CETengrism Changshi 1335–1338 CETengrism Yesun Temur 1338–1342 CETengrism Ali Sultan 1342 CE Islam Muhammad I ibn Pulad 1342–1343 CE Islam Qazan Khan ibn Yasaur 1343–1346 CE Islam Qazan's death signified the end of the effective power of the Chagatai khans within the ulus; subsequent khans were rulers in name only. Qazaghan took the title of Amir and to legitimize himself conferred the title of khan on descendants of Genghis Khan of his own choosing. Danishmandchi Under Qazaghan 1346–1348 CE Islam During Qazaghan's reign the Chagatai Khanate devolved into a loose confederation of tribes. This resulted in the Division of the Empire in 1347 CE into the Western Chagatai Khanate and Eastern part known as Moghulistan under Tughlugh Timur.

Blue rows signifies nominal rule.

Khans of the Western Chagatai Khanate and the Eastern Chagatai Khanate (Moghulistan)

Western Chagatai Khanate MoghulistanBayan Qulï Under Qazaghan & Abdullah bin Qazaghan1348–1358 CETughlugh Timur 1347–1360 CEShah Temur Under Abdullah bin Qazaghan1358 CETughlugh Timur (Tribes of Chagatai Khanate rebelled against Abdullah bin Qazaghan who was of the Qara'unas forcing him to retreat but the coalition of Suldus under Buyan Suldus and Barlas under Hajji Beg collapsed; anarchy reigned in Chagatai Khanate. This power vacuum allowed Tughlugh Timur to move in without much resistance only Hajji Beg who was defiant had to make his escape. Tughlugh Timur then appointed Timur Gurkani as Chief of Barlas tribe and returned to his capital. However he was back in the region next year with the view of removing most Amirs and to consolidate his grip on his new conquered territory. He executed several amirs, including Amir Bayazid and Buyan Suldus. The son of Abdullah bin Qazaghan named Amir Husayn was the new Chief of the Qara'unas and resisted the powerful King of Moghulistan but was also defeated, however he would return after the king's death.Tughlugh Timur before leaving for his capital left his son Ilyas Khoja as viceroy of Chagatai Khanate region. The ruthlessness with which the Moghuls ruled the region caused many to oppose them, including Amir Husayn of the Qara'unas and Timur of the Barlas. Together they faced an army of Moghuls and local tribes loyal to Ilyas Khoja, and defeated them. Shortly afterwards, Tughlugh Timur died and Ilyas Khoja left for Moghulistan to take power. The tribes nominated and placed Adil-Sultan as nominal Khan of Chagatai Khanate. 1361–1363 CE Adil-Sultan Under Tribal Confederation of Amir Husayn and Amir Timur1363 CEIlyas Khoja 1363–1368 CEKhabul Shah Under Amir Husayn1364–1370 CEQamar-ud-din Khan Dughlat Usurper1368–1392 CESoyurgatmish Under Amir Timur1370–1388 CE Sultan Mahmud Khan Under Amir Timur. Sultan Mahmud's death in 1402 marked the effective end of the line of Chagatai Khans in Transoxiana, who had long been mere figureheads and the rise of Timurid dynasty. 1388–1403 CEKhizr Khoja 1389–1399

Transoxiana remained in the hands of Timur and his successors. For a continued list of rulers of Moghulistan see below.

Khans of Moghulistan

Titular Name(s) Personal Name ReignKhan Tughlugh Timur 1348–1363 CEKhan Ilyas Khoja1363–1368 CEKhan Qamar-ud-din Khan Dughlat1368–1392 CEKhan Khizr Khoja1389–1399 CEKhan Shams-i-Jahan1399–1408 CEKhan Muhammad Khan1408–1415 CEKhan Naqsh-i-Jahan1415–1418 CEKhan Uwais Khan1418–1421 CE1st reignKhan Sher Muhammad1421–1425 CEKhan Uwais Khan1425–1429 CE2nd reignKhan Satuq Khan1429–1434 CEKhan Esen Buqa II1429–1462 CE Division of Moghulistan into Western Moghulistan (Yarkent) and Eastern Moghulistan (Turpan) Green shaded row signifies rule of usurper.

Khans of Western Moghulistan (Yarkent) and Khans of Eastern Moghulistan (Turpan)

Western Moghulistan (Yarkent Khanate) Eastern Moghulistan (Turpan Khanate)Yunus Khan1462–1469 CEDost Muhammad Khan 1462–1468 CEKebek Sultan Oghlan 1469 CEYunus Khan 1469–1487 CEMahmud Khan 1487–1508 CEAhmad Alaq 1487–1503 CEMansur Khan 1503–1508 CEMansur Khan 1508–1514 CE Sultan Sa'id Khan 1514–1533 CEMansur Khan 1514–1543 CEAbdurashid Khan 1533–1560 CEShah Khan 1543–1570 CEAbdul Karim Khan (Yarkand) 1560–1591 CE Muhammad Sultan (Yarkand) 1592-1609 CE Shudja ad Din Ahmad Khan (Yarkand) 1609-1618 CEAbul Muhammad Khan (Turpan) 1570 CE Sufi Khan (Turpan) 1570 CE Sultan Sa'id Khan after defeating Mirza Abu Bakr Dughlat established the Altishaher or union of 6 cities, a much reduced western half of Moghulistan. By this time the western half was referred to as Kashgaria and eastern half was referred to as Uyghurstan. During the reign of Abdurashid Khan a certain Naqshbandi Sufi teacher Ahmad Kasani (1462–1542), known as Makhdum-i-Azam (the Great Master) came to Kashgar from Samarkand. His descendants, known as Makhdum Zadas and bearing title "Khoja", would play an important role in the history of the region from the 16th to 19th centuries. Makhdum's eldest son Muhammad Amin, known also as Khoja Kalon (d.1598) became the founder of Sufi order (tariqa) Ishkiyya of Nakshbandi Khojagan, his son Muhammad Yūsuf (d.1653) settled himself in Kashgar and was granted village of Bashkerim near Kashgar by Abdullah Khan in 1638. His son Khoja Hidayatullah better known as Afaq Khoja and his followers became known as the Aq Taghliks, those of the "White Mountains", because of their close approximation to Tangri Tagh (Tian Shan). Makhdum's second son, Muhammad Ishaq Wali (d.1599 in the age of 94), founder of Ishaqiya Sufi order of Nakshbandi Khojagan, with his followers established themselves in Yarkand and became known as the Qara Taghliks, those of the "Black Mountains", because of their close approximation to the Pamir, Karakoram and Kunlun. The Kashgaria region gradually devolved into small city states with the Khojas as rivals post 1570 CE Said Khan successors (Yarkent Khanate)

Abdurashid Khan (in Aksu 1521–1533) 1533–1560, son of Sultan Said Khan Abdul Karim Khan (Yarkand) 1560–1591, eldest son of Abdurashid Khan Muhammad Khan (in Turfan 1588–1591) 1591–1610, 5th son of Abdurashid Khan, in 1603 was visited in Yarkand by Portuguese Jesuit Bento de Gois, who was searching land ways from India to Ming China, headed trade mission on behalf of Moghul Emperor of India Akbar the Great and had a Letter of Safe Conduct, granted by Akbar and addressed to Muhammad Khan, with him. Shudja ad Din Ahmad Khan 1610–1618, son of Muhammad Khan, grandson of Abdurashid Khan, was killed in 1618 during hunting Kuraysh Sultan 1618, son of Yunus Sultan, grandson of Abdurashid Khan, ruled only 9 days before he was killed Abd al-Latif (Afak) Khan 1618–1630, second son of Shudja ad-Din Ahmad Khan, who was only 13 when was set up on khanship, died in the age of 25 Sultan Ahmad Khan (Pulat Khan) 1630–1633, first son of Timur Sultan, who was the first son of Shuja ad-Din Ahmad Khan and died in 1615 Mahmud Sultan (Qilich Khan) 1633–1636, second son of Timur Sultan, died in the age of 22 when was poisoned in 1636 by Khoja Yahiya (died in 1646), son of Khoja Ishak, founder of Ishakiyya branch of Nakshbandi Khojagan Sufi Order, followers of which were known as Kara Taghliks. Sultan Ahmad Khan (Pulat Khan) 1636–1638, restored on khanship with help of Khoja Yahiya, who was granted village Guma near Khotan by Sultan Ahmad Khan, resigned in 1638 on demands of emirs in favor of Abdullah Khan, died in 1640 in the age of 27 Abdullah Khan (in Turfan 1634/5–1638/9) 1638–1669, eldest son of Abduraim Khan, grandson of Abdurashid Khan, expelled to India in 1669, where he was received by Moghul Emperor Aurangzeb, who arranged his Hajj to Mecca, died in 1675 in the age of 67, buried in Agra Nur ad-Din Sultan ( in Aksu 1649–1667) 1667–1668 in Kashgar and Yengisar, youngest son of Abdullah Khan, died in 1668 in the age of 31, 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, 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, eldest son of Abdullah Khan, disciple of Ak Taghlik Khoja Mohammad Yusuf 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 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 2 April 1670 by Kara Taghliks, expelled Appak Khoja and his son Yahia Khoja from the country in 1670, in 1678 captured by Dzungars, who were invited by Ak Taghlik leader Appak Khoja using recommendation letter from 5th Dalai Lama, died in Ili River Valley ( Baghistan) in 1680 in the age of 56. Abd ar-Rashid Khan II (in Turfan 1680–1682) 1678–1680, eldest son of Sultan Said Baba Khan, set up on khanship by Dzungar Galdan Boshugtu Khan, who came to Yarkand with Appak Khoja. Muhammad Imin Khan (Muhammad Amin Khan) (in Turfan 1682–1690) 1680–1681 in Chalish, second son of Sultan Said Baba Khan Appak Khoja 1680–1690, died in 1694, set up himself on khanship after expelling Abd ar-Rashid Khan II from Yarkand with help of Dzungars, expelled Kara Taghlik leader Khoja Daniyal into Kashmir. Muhammad Imin Khan (Muhammad Amin Khan) 1690–1692, was recalled from Turpan and elected a Khan on Kurultai of Kashgar and Yarkand Beks, was killed in 1692 after losing a battle with Appak Khoja near Kargalik Yahiya Khoja (in Kashgar 1690–1692) 1692–1695, son of Appak Khoja, set up on khanship by Appak Khoja, killed in 1695 by Hanim Pasha Hanim Pasha (Hanum Padshah) 1695, sister of Muhammad Imin Khan, widow of Appak Khoja, was killed in 1695 Akbash Khan 1695–1705, 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 to resist Ak Taghliks and Dzungars, fled to India in 1705