List of Chagatai khans

The Chagatai Khans were the heads of the Chagatai ulus 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.''

Khans of Chagatai Khanate

 * Blue rows signifies nominal rule.

Khans of Western Chagatai Khanate ahd Khans of Moghulistan (Eastern Half)

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

Khans of Mughalistan

 * Green shaded row signifies rule of usurper.

Said Khan successors- Moghul Khans of Yarkant Khanate (1465-1759)
The remnants of the state fell to the Aqtaghlyq branch of Khojas, a confederation under the influence of the Dzungars. ''In 1713 remnant of Yarkant Khanate - Altishar ( union of 6 cities), became dependency of Dzungar Khanate. In 1752 it restored independence after revolt against Dzungar Khanate. In 1759 was conquered by Qing China.''
 * 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 and had Letter of safe conduct, granted by Moghul Emperor Akbar, with him.
 * Shudja ad-Din Ahmad Khan 1610-1618, son of Muhammad Khan
 * Kuraish Sultan 1618, son of Yunus, grandson of Abdurashid Khan
 * Abd al-Latif (Afak) Khan 1618–1630, second son of Shudja ad-Din Ahmad Khan
 * Sultan Ahmad Khan (Pulat Khan) 1630-1633, 1636-1638, son of Timur Sultan, grandson of Shudja ad-Din Ahmad Khan
 * Mahmud Sultan (Qilich Khan) 1633–1636, brother of Sultan Ahmad Khan, son of Timur Sultan, grandson of Shudja ad-Din Ahmad Khan
 * Abdullah Khan(Moghul 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, died in 1675, buried in Agra
 * Nur ad-Din 1669, youngest son of Abdullah Khan
 * Ismail Khan (Moghul khan) (in Aksu 1666–1670) 1669, 5th son of Abduraim Khan
 * YuIbars 1669–1670, eldest son of Abdullah Khan
 * Ismail Khan (Moghul khan) restored in 1670–1678, in 1678 captured by Dzungars, who were invited by Appak Khoja, died in Ili in 1680
 * Abd ar-Rashid Khan II (in Turfan 1680–1682) 1678–1680, son of Sultan Said Baba Khan
 * Muhammad Imin Khan (in Turfan 1682-1694) 1680-1681, son of Sultan Said Baba Khan
 * Appak Khoja 1681–1692, died in 1694
 * Yahya Khoja 1692–1695, son of Appak Khoja, died in 1695
 * Muhammad Mumin Khan( Akbash Khan) 1695-1705, son of Sultan Said Baba Khan, fled to India

Mansur Khan successors in Uyghurstan
''Annexed by the Dzungars. After exterminating of Dzungar Khanate by Qing China in 1756, remnants of Dynasty survived in semi-autonomous Kumul Khanate till the 20th century, last ruler of which  Maqsud Shah died in 1930.''
 * Shah Khan 1543–1570, eldest son of Mansur Khan
 * Koraish Sultan or Kuraysh, son of Abdurashid Khan (Khotan 1533–1588; Chalish 1570–88) 1570–1588, 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.
 * Muhammad Khan (in Kashgaria 1591–1610), 1588–1591, son of Abdurashid Khan
 * Abduraim Khan 1591-1636, youngest son of Abdurashid Khan
 * Muhammad Khashim (in Chalish) 1608–1610
 * Abdullah Khan (in Chalish, in Kashgaria 1638–1669) 1636-1638, eldest son of Abduraim Khan
 * Abu'l Muhammad Khan 1636–1653, son of Abduraim Khan
 * Sultan Said Baba Khan 1653 d. 1680, son of Abduraim Khan
 * Ibrahim 1653–1655
 * Sultan Said Baba Khan (restored) 1655–1680
 * Abd ar-Rashid Khan II (in Chalish 1678–1680) 1680–1682, eldest son of Sultan Said Baba Khan, died in 1694
 * Muhammad Imin Khan 1682-1694, son of Sultan Said Baba Khan