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Tughlugh Timur Khan (1312/13–1363) was the Khan of Moghulistan from c. 1347 and Khan of the whole Chagatai Khanate from c. 1360 until his death. Esen Buqa is believed to be his father. His reign is known for his conversion to Islam and his invasions of Transoxiana.
Ahmad Alaq was the Khan of Eastern Moghulistan from 1487 to 1504. He was the second son of Yunus Khan. His mother was Shah Begum, fourth daughter of Badakhshan prince Lali.
Esen Buqa I was Khan of the Chagatai Khanate. He was the son of Duwa.
Esen Buqa II was Khan of Moghulistan from 1429 until his death. He was the younger son of Uwais Khan.
Yunus Khan, was Khan of Moghulistan from 1462 until his death in 1487. He is identified by many historians with Ḥājjī `Ali, of the contemporary Chinese records. He was the maternal grandfather of Babur, founder of the Mughal Empire.
Sultan Mahmud Khan, was Khan of Tashkent and of the Moghuls of western Moghulistan (1487–1508). He was the eldest son of Yunus Khan. He was born in 1464, his mother was Shah Begum, daughter of Badakhshan prince Lali, who claimed his descent from Alexander the Great and gave one of his six daughters to Yunus Khan in marriage, pleasing his request.
Sultan Said Khan ruled the Yarkent Khanate from September 1514 to July 1533. He was born in the late 15th century in Moghulistan, and he was a direct descendant of the first Moghul Khan, Tughlugh Timur, who had founded the state of Moghulistan in 1348 and ruled until 1363. The Moghuls were turkicized Mongols who had converted to Islam.
Abdurashid Khan, (1508-1560) was the ruler of the Yarkent Khanate.
Mirza Muhammad Haidar Dughlat Beg was a Chagatai Turco-Mongol military general, governor of Kashmir, and a historian. He was a Mughal Dughlat prince who wrote in both Chaghatai and Persian languages. Haidar and Babur were cousins on their mother's side, through the line of Genghis Khan. Unlike Babur, Haidar considered himself more of an ethnic Mongol of Moghulistan.
Muhammad Haidar Mirza was the Dughlat amir of Kashgar from c. 1465 until 1480. He was the grandfather and namesake of the historian Muhammad Haidar Mirza (1499/1500-1551).
The Dughlat clan was a Mongol clan that served the Chagatai khans as hereditary vassal rulers of several cities in western Tarim Basin, in modern Xinjiang, from the 14th century until the 16th century. The most famous member of the clan, Mirza Muhammad Haidar, was a military adventurer, historian, and the ruler of Kashmir (1541–1551). His historical work, the Tarikh-i Rashidi, provides much of the information known about the family.
Uwais Khan ibn Sher Ali also referred to as Sultan Vais Khan, was the Moghul Khan of Mughalistan;. He was the nephew of Sher Muhammad. In English, his name has been variously spelled and pronounced as either Awais, Owais or Vais.
Yesünto'a was the third son of Mutukan, and grandson of Chagatai, founder of the Chagatai Khanate. His brothers were Yesü Möngke and Baidar. His nephew Alghu son of Baidar and his brother Yesu Mongke, both were the Khans of the Chagatai Khanate, as were Yesünto'a's sons Qara Hülëgü and Baraq (1266–1271).
Khizr Khwaja Khan was the son of Tughlugh Timur and Khan of Moghulistan during the Chagatai Khanate, reigning from 1390 to 1399 AD.
Muhammad Khan was a son of Khizr Khoja and was Khan of Moghulistan from 1408 to 1415.
In the early 16th century, Sultan Mahmud Khan, the Chagatai Khan of Western Moghulistan, and Sultan Ahmad Alaq Khan, the Chagatai Khan of Eastern Moghulistan, decided to counter the growing power of the Uzbeks under Muhammad Shaybani. Sultan Ahmed Tambol had rebelled against his Timurid master Babur and declared his independence. But when Babur tried to reconquer his territory with the help of his uncles, Ahmed Tambol sought the assistance of the Uzbeks. The two Moghul brothers united their forces and launched a campaign against Tambol, but Muhammad Shaybani surprised the Khans and proved victorious in battle of Akhsi and took them both prisoner.
Muhammad Sultan was 5th son of Abdurashid Khan and became Khan of Yarkent Khanate from 1592 to 1609 after the death of his elder brother Abdul Karim Khan. He was the ruler who arranged Jesuit Bento de Goes' Caravan, sent by the third Mughal emperor Akbar in 1603, to the border of the Ming dynasty. Gois came to Yarkand in November 1603, was received by Muhammad Khan and spent in the country almost one and a half year, visiting Khotan, Aksu, Kucha, Chalish and Turpan. Gois mentioned that Muhammad Khan was governing the country through his direct relatives like Hen sitting on eggs in the nest , he also indicated that Chalish had very strong fortress, here he had open dispute with local ruler about the God and religion. Some of his diaries were published in Koln in 1618. In 1605 envoy from Abbas I of Persia came to Yarkand with offer to conclude an alliance against Shaybanids, result of negotiations is unknown. Muhammad Khan intensified relations of Yarkand Khanate with Moghul Empire in India, Emperor Akbar sent envoy Shah Muhammad to Yarkand and wrote in one of his letters to Muhammad Khan, that India is a great country, consisting of 7 climates, and Kashmir is under protection of this country, he expressed his desire to establish trade relations with the Ming dynasty and asked Muhammad Khan to help on this matter.
Mutukan was the eldest son of Chagatai Khan and a grandson of the founding Mongol khagan Genghis Khan. Mutukan (Mö'etüken) was killed during the siege of Bamiyan in 1221. His son was Yesü Nto'a. Yesu' Nto'a was the father of Baraq. Buraq Khan was khan of Moghulistan from 1266 to 1271.
Shah Shujaʿ al-Din Ahmad Khan was the Khan of the Yarkent Khanate after death of his father Muhammad Sultan from 1609 to 1618.
Mihr Nigar Khanum was the first wife of Sultan Ahmed Mirza, the King of Samarkand and Bukhara. She was a princess of Moghulistan by birth and was the eldest daughter of Yunus Khan, the Great Khan of Moghulistan and his chief consort Aisan Daulat Begum. She was also the aunt of Emperor Babur, the founder of the Mughal Empire of India as well as its first Emperor.