Yakub Beg rules at the height of The Great Game era, when the British, Russian, and Manchu Qing empires are all vying for Central Asia.

His domain, Kashgaria, extends from the capital, Kashgar, in southwestern Xinjiang to Ürümqi, Turfan, and Hami in central and eastern Xinjiang more than a thousand kilometers to the northeast, including a majority of what is known at this time as East Turkestan.

Yaqub Beg and his Turkic Uyghur Muslims also declare a Jihad against Chinese Muslims in Xinjiang.

Yaqub goes as far as to enlist Han Chinese to help fight against Chinese Muslim forces.

Turkic Muslims also massacre Chinese Muslims in Ili.

The great Dungan Revolt, or insurrection of the Chinese Muslims, which had broken out in 1862 in Gansu, had spread rapidly to Zungaria and through the line of towns in the Tarim basin.

The Dungan troops in Yarkand had risen and massacred some seven thousand Chinese on August 10, 1863, while the inhabitants of Kashgar, rising in their turn against their masters, had invoked the aid of Sadik Beg, a Kyrgyz chief, who had been reinforced by the Naqshbandi shaykh Buzurg Khan (Busurg Khan) (the heir and only surviving son of Jahangir Khoja) of the White Mountain, and Yakub Beg, his general, these being dispatched at Sadik's request by the ruler of Kokand to raise what troops they could to aid Muslims in Kashgar.

Sadik Beg had soon repented of having asked for a Khojah, and had eventually marched against Kashgar, which by this time had succumbed to Buzurg Khan and Yakub Beg, but had been defeated and driven back to Khkand.

Buzurg Khan had delivered himself up to indolence and debauchery, but Yakub Beg, with singular energy and perseverance, has made himself master of Yangi Shahr, Yangi-Hissar, Yarkand, and other towns.

By 1865, Yakub Beg had become the commander-in-chief of the army of Kokand.

Taking advantage of the Hui uprising in China's Xinjiang province, he has led his Andijani army to capture Kashgar and Yarkand from the Chinese and gradually takes control of most of the region, including Aksu, Kucha, and other cities in 1867.

He then deposed his former master, Buzurg Khan, and declared himself Amir of Kashgaria.

For the first few years, he had been a vassal of the Khan of Kokand, but eventually declares independence.