In Baltistan (presently under Pakistani occupation) -- the area adjoining Ladakh -- it is believed that Islam was introduced by Amir Sayyid Ali Hamadani, popularly known in Kashmir as Shahi Hamdan. He first visited Kashmir during the reign of Sultan Shahabuddin (1360-1375). In the forties of the 15th century, Sayyid Mohamed Nurbaksh, a grandson of Amir Hamadani came to Baltistan from Turkestan. He was largely instrumental in introducing Islam in Baltistan and other parts of Ladakh. Many mosques were built by him. He visited Skardu, Shigar and Khaplu, first converting the rulers and nobles into Islam, after which the masses followed suit. Thus Islam soon replaced Buddhism in Baltistan and adjoining regions.

It was towards the end of the 14th century that some Muslim missionaries settled down in parts of the present Kargil District and propagated Islam. In the second half of the last century, Raja Kunga Namgyal of Suru Kartse married his son to a Muslim princess of Skardu. A batch of missionaries came with her and they were instrumental in converting almost the entire population of Suru Kartse to Islam.

Missionaries from Gilgit are believed to have converted the population of Shingo, Shigar and Dras to Islam.