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It appears from different traditions that the virtual penetration of the Ithna Asharism in Gilgit took place around 955/1548, and we have observed hitherto that Raja Mirza Khan (1565-1600), the 7th ruler of Trakhan dynasty in Gilgit, had espoused Ithna Asharism. Later on, Mir Ayesho Khan II assumed the power and married to Shah Khatoon, the daughter of Abdal Khan of Skardu and Baltistan. Thus the matrimonial tie engendered close relation and communication between the people of Hunza and Baltistan. From the time of Mir Ayesho Khan II down to the period of Mir Saleem Khan II, the inhabitants of Gilgit and Hunza adhered to the Ithna Asharism for about 300 years. Mir Saleem Khan II is reported to have embraced Ismailism by the hands of a certain Ismaili dai of Badakhshan, called Sayed Shah Ardbil. Mir Saleem Khan however did not divulge his new faith and exercised taqiya for some political reasons until his death in 1240/1823. His son and successor, Mir Ghazanfar Ali Khan is said to have invited another Ismaili dai from Badakhshan, called Sayed Hussain Ardbil, the son of Sayed Shah Ardbil, so that the Ismailism could be thoroughly penetrated in Gilgit and Hunza during his period.
In 1255/1838, Mir Ghazanfar Ali Khan dispatched his emissary, Akhund Turab Ali to Badakhshan to bring Sayed Hussain Ardbil in this context. He also sent his vizir, Zinat Ali Shah to receive Sayed Hussain with great pomp at the outskirts of Hunza. The tradition has it that Zinat Ali Shah feted warm welcome to the Ismaili dai and became the first convert publicly. It however reprobated Akhund Turab Ali, who rushed back to Hunza quietly and aroused Mir Ghazanfar Ali Khan that the ruler should be enlisted as a first convert. Thus, Mir Ghazanfar Ali Khan did not embrace Ismailism and restricted the missionary activities of the Ismaili dai in his region. Sayed Hussain found the atmosphere not congenial, therefore, he quietly returned to Badakhshan.

In the meantime, Sayed Yaqut Shah, the son of Sayed Shah Abdur Rahim visited Kirman to see the Aga Khan I. His ancestors had propagated Ismailism in Badakhshan for considerable period, and some of them also ruled Wakhan and Zebak. Sayed Yaqut Shah disclosed a plan of his proselytising mission in Gilgit and Hunza, which met the approval of the Imam. At length, he arrived in Hunza in 1254/1838 after passing through Herat, Kokand and the valley of Sirikol. This time, Mir Ghazanfar Ali Khan treated the Ismaili dai with due consideration and embraced Ismailism. He was followed by his attendants and the inhabitants of Hunza. Sayed Yaqut Shah strode a brisk mission at full swing. Since his mission was spread over the territories of Turkistan, Badakhshan and Chitral, he was unable to prolong his stay in Hunza, and after 25 days of his arrival, he returned to his native land. He had however left behind some responsible elders in each village, known as the khalifa, who imparted the cardinal principles of the Ismaili doctrine to the new converts.

Meanwhile, Sayed Ghulam Ali Shah, the son of Sayed Hussain Ardbil also arrived in Hunza and joined the mission work spread by Sayed Yaqut Shah. He was also followed by other well-known dais, such as Khwaja Shah Talib, Mirza Ismail, Khwaja Shahid, etc.

Mir Ghazanfar Ali Khan died in 1281/1864 and was succeeded by his son, Mir Muhammad Ghazan Khan I, whose successor Mir Safdar Ali Khan had to take refuge in Shagnan during the British invasion in 1308/1891. The British commissioned his half-brother, Mir Muhammad Nazim Khan as the ruler of Hunza. He was followed by Mir Muhammad Ghazan Khan II and then Mir Muhammad Jamal Khan, the last Ismaili ruler of Hunza, who died in 1976. It must be known on this juncture that the entire area, including Gilgit, Hunza and Baltistan was known as Gilgit Agency till 1947. Sandwiched between the high peaks of Hindukush and Karakorum on the north and those of western Himalaya on the south, is called now the Northern Areas of Pakistan, which might also be called the Trans-Himalaya Districts of Pakistan. It covers an expanse of about 27,188 square miles, thickly populated by the Ismailis.