The following observation was made by a religious dignitary called Mauláná Muhammad Kázi:[3] I had heard that Yunus Khán was a Moghul, and I concluded that he was a beardless man, with the ways and manners of any other Turk of the desert.

Abu Sa'id had become annoyed with the frequent raids that the Moghuls under Esen Buqa made into his territory and wanted to put an end to the menace.

Shortly afterwards, he sent one of the most respectable Sayyids of Kashgar, Amir Zia-ud-Din, to Badakhshan to meet Shah Sultan Muhammad Badakhshi and seek one of his six daughters in marriage.

Shah Sultan Muhammad Badakhshi (also known as "Prince Lali") was believed to be a direct descendant of Iskandar Zulkarnain (Alexander the Great), son of Filikus Rumi (Philip II of Macedon), who according to (dubious) legend left one of his sons in the isolated mountain country out of reach of rivals in hope that his progeny would continue his dynasty in the East.

He entrusted his fourth daughter, Shah Begum, to Sayyid Zia-ud-Din, who brought her back with him to Kashgar and delivered her over to Yunus Khan, and the wedding was celebrated with due ceremony.

The Timurid ruler Abu Sa'id had been Yunus Khan's great mentor in life, who had called him from obscurity and exile in Iran and bestowed lands and an army upon him.

The amirs were apparently upset over Yunus Khan's desire to reside in towns and abandon the traditional nomadic way of life.

He demonstrated these qualities strikingly when he gave Yunus Khan's first wife, Isan Daulat Begum, maternal grandmother of Babur, as a present (or booty of war) to his officer Khoja Kalan.

Some time after this event, Shaikh Jamal himself was killed by Moghul amirs and Yunus Khan was restored, after promising not to live in towns but follow the nomadic way of life.

Shortly afterwards, after learning that Kebek Sultan (the young son of Dost Mohammad) had been killed by his followers, Yunus Khan to take control of Eastern Moghulistan (Uyghurstan).

He forged ties of kinship with most of the prominent Timurids; three of Yunus Khan's daughters were given in marriage to three sons of his former mentor Abu Sa'id.

Yunus Khan kept on especially friendly terms with his second son-in-law, Umar Shaikh Mirza II, and it was Umar Shaikh who usually gave his father-in-law territory to reside in during the winters (the Timurids were settled in towns and ruled the attached provinces; Yunus Khan, after having promised his amirs to maintain the nomadic lifestyle, kept his word).

Being of a rather unworldly and poetic temperament, Umar Shaikh II often needed the help of his father-in-law to deal with his own elder brother, Ahmad Mirza, with whom his relations had been bad since childhood for no particular reason.

In 1484, Yunus Khan took advantage of one of the periodic conflicts between Sultan Ahmad and Umar Shaikh Mirza II to take possession of Tashkent.

This had been a constant issue for him, due to the fact that his life until almost the age of forty had been spent in large cosmopolitan Persian cities like Yazd and Shiraz.

His decided to live in the city for at least a prolonged period, a decision which upset the other Moghuls, and many of them left for Moghulistan under the leadership of Yunus' own son Ahmad Alaq.