As with other regions of the world, Kashmir was home to intense Sunni and Shia conflicts with the dominant Sunni Muslim community often persecuting the Shia Muslims of Kashmir, particularly in the 16th century.
The first Muslims in Kashmir were predominantly Sunni Muslims belonging to the Hanafi School. However, towards the end of the 15th century, a Shia preacher named Shams ud-Din arrived in Kashmir to spread his Shia philosophy. Much to his disappointment, the Sunni Ulema (religious scholars) and influential political leaders of Kashmir, including Sayyid Muhammad Baihaqi, persecuted him and his followers so much that they fled Kashmir.
Later, following the conquest of Kashmir by Mirza Haider Dughlat, who was a Turco-Mongol military general and cousin of Mughal Emperor Babur, Shias were once again persecuted because he believed that uniformity of religion was important for stability in Kashmir. He proceeded to put many Shia religious figures in Kashmir to death and banned Shia Islam entirely.
While sectarian persecution in Kashmir often involved Sunnis persecuting Shias, there were incidents during the rule of the Chaks, who were Shias, where Sunnis were persecuted. One Sunni scholar was even put to death for refusing to include Shia prayers in a Sunni-dominant mosque.
The persecution of Sunnis during the Chak rule had devastating repercussions for Kashmir because Sunni Kashmiri chiefs and religious figures went to visit Akbar, the Mughal Emperor, and asked him to invade and conquer Kashmir to rid it of Shia rulers. In short, Islamic sectarian violence, particularly in the 16th century, resulted in Kashmir losing its autonomy to the Mughal Empire.