| | | | | | | Genghis Khan Great Khan of the Mongol Empire 1206–1227 | | | | | | | | | | | | |
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| Jochi | | Chagatai Khan Khan of the Chagatai Khanate 1226–1242 | | Tului | | | | | | Ogedei Khan Great Khan of the Mongol Empire 1229–1241 | |
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| | | | Yesü Möngke Khan of the Chagatai Khanate 1246–1252 | | Baidar | | Sarban | | Khashi | | | | |
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Mutukan | | | | | Alghu Khan of the Chagatai Khanate 1260–1266 | | Negübei Khan of the Chagatai Khanate 1270–1272 | | Khaidu | | | | |
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Büri | | Qara Hülegü Khan of the Chagatai Khanate First Reign 1242–1246 Second Reign 1252 | | Yesünto'a | | | | | Danishmendji[1] Khan of the Chagatai Khanate 1346–1348 | | Ali Sultan[2] Khan of the Chagatai Khanate 1342 |
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Qadaqchi | | Mubarak Shah Khan of the Chagatai Khanate First Reign 1252–1260 Second Reign 1266 | | Baraq Khan Khan of the Chagatai Khanate 1266–1270 | | | | | Soyurgatmish[3] Khan of the Western Chagatai Khanate 1370–1384 |
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Buqa Temür Khan of the Chagatai Khanate 1272–1282 | | Taliqu Khan of the Chagatai Khanate 1308–1309 | | Du'a Khan of the Chagatai Khanate 1282–1307 | | | | | Sultan Mahmud[3] Khan of the Western Chagatai Khanate 1384–1402 |
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Orüg Temür | | Konchek Khan of the Chagatai Khanate 1307–1308 | | Kebek Khan of the Chagatai Khanate First Reign 1309–1310 Second Reign 1318–1325 | | Eljigidey Khan of the Chagatai Khanate 1325–1329 | | Esen Buqa I Khan of the Chagatai Khanate 1310–1318 | | Du'a Temür Khan of the Chagatai Khanate 1329–1330 | | Tarmashirin Khan of the Chagatai Khanate 1330–1334 | | Ebugen | | | | Surguda |
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Yasa'ur | | Pulad | | | | | | Khabul Shah Khan of the Western Chagatai Khanate 1364–1370 | | Tughlugh Timur Khan of Moghulistan 1347–1363 Khan of the Chagatai Khanate 1360–1363 | | Buzan Khan of the Chagatai Khanate 1334–1335 | | | | Changshi Khan of the Chagatai Khanate 1335–1338 | | Yesun Temür Khan of the Chagatai Khanate 1338–1342 | | Bayan Quli Khan of the Western Chagatai Khanate 1348–1358 |
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Qazan Khan Khan of the Chagatai Khanate 1343–1346 | | Muhammad I Khan of the Chagatai Khanate 1342–1343 | | | | | | | | Ilyas Khoja Khan of Moghulistan 1363–1368 | | Khizr Khoja Khan of Moghulistan 1389–1399 | | | | | | | | | | Shah Temur Khan of the Western Chagatai Khanate 1358 |
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| | | | Adil Sultan Khan of the Western Chagatai Khanate 1363 | | | | | | | | | | Shams-i-Jahan Khan of Moghulistan 1399–1408 | | Muhammad II Khan of Moghulistan 1408–1415 |
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| | | | | | | | | | | | | | | | Naqsh-i-Jahan Khan of Moghulistan 1415–1418 | | Sher Ali Oghlan[4] | | Sher Muhammad Khan of Moghulistan 1421–1425 |
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| | | | | | | | | | | | | | | | | | | | Vais Khan Khan of Moghulistan First Reign 1418–1421 Second Reign 1425–1429 |
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| | | | | | | | | | | | | | | | | | Yunus Khan Khan of Eastern Moghulistan 1462–1487 Khan of Moghulistan 1469–1487 | | Esen Buqa II Khan of Moghulistan 1429–1462 |
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| | | | | | | | | | | | | | Ahmad Alaq Khan of Kyrgyz Khanate 1487–1503 | | Mahmud Khan Khan of the Western Moghulistan 1487–1508 | | Dost Muhammad Khan of Uyghuristan 1462–1468 |
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| | | | | | | | | | | | Sultan Said Khan[5] Khan of the Western Moghulistan 1514–1533 | | Mansur Khan Khan of Uyghuristan 1503–1543 Khan of Moghulistan 1508–1514 | | | | Kebek Sultan Oghlan Khan of Uyghuristan 1469 |
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| | | | | | | | | | | | Khans of Yarkent | | Shah Khan Khan of Uyghuristan 1543–1560 | | Muhammad Khan[6] Khan of Uyghuristan ?–1570 |