In the second half of the 16th century, in the northern-most part of the Empire’s European province of Bosnia, the Ottoman authorities carried out two waves of ruthless persecutions of the members of the Melami-Bayrami Sufi order, which included the execution of the leader and spiritual pole of the order, Sheikh Hamza Bali. At the same time, several similar kinds of persecutions took place deep inside central Anatolia against the Kizilbas and their suspected sympathisers. Two very different groups of religious subalterns at two completely opposite ends of the Empire, one, an esoteric Sufi order with only some Shi’a tendencies, with strong urban support and links with artisans and trade-guilds, and the other, a militant Shi’a movement with rural power-base and strong links with the neighbouring Safavids, were seemingly afforded very similar treatment by the Ottoman authorities. The information on both sets of persecutions is contained in fetvas and investigation or arrest warrants (hüküms) contained in the Ottoman ‘registers of important affairs’ (mühimme defterleri). The present paper will examine a sample of these documents in order to ascertain the extent to which the Ottoman government and its officials who composed them saw these two groups as parts of the same phenomenon. It will compare the manner in which some of these investigations took place, the wording of the arrest warrants and/or fetvas, and the terminology used to describe the members and sympathisers of the two groups. It will argue that the similarities between the documents – apart, of course, from demonstrating that the government used a certain template for certain types of affairs – also reveal a level of detachment by the Ottoman officials in dealing with these groups. It will further argue that, although the Ottoman government went to great lengths to justify these persecutions on religious grounds, e.g. defining specific terminology to describe the members of these groups, the formulaic and often sweeping manner in which this justification was applied demonstrates that the political and security concerns were of more pressing importance than the ostensive religious ones.