The article examines the history of the development of the nationalist movement of Malay Muslims living in the south of Thailand, which is more than half a century old and is a demonstration of their identify in conditions of being in an alien and even hostile religious, cultural and ethnic environment and a form of protest against the government policy of forced assimilation. The desire of Malay Muslims for independence, which has taken the form of armed resistance to the central government, is a response to the marginalization of their economic and political position and to the discriminatory policy of the government. Separatism as an ideology of ethno-nationalism and as a political movement of Malay Muslims, which originated in the 1940s of the last century, has transformed in the last fifteen years into a religious jihad with an accompanying increase in violence. It is based on small groups of militant separatists recruiting their supporters from students of traditional Muslim schools. Having almost completely abandoned political activity, the separatists concentrated on carrying out acts of terror. With the emergence of ISIS and its attempts to create its base in the Muslim countries of Southeast Asia, a threat arose that a local conflict would develop into a transnational one. However, local jihadists, following the interests of self-survival and adhering to a nationalist ideology, show their distance from ISIS, avoiding involvement in the international terrorist movement. The author notes that despite the limited social base of terrorist separatist groups, the idea of independence remains widely demanded in local socie ty. The prolonged nature of the ethno-religious conflict poses the task to resolve it by Thai government. Attempts to suppress the separatism of Malay Muslims by force have been unsuccessful, which prompts the Thai government to look for political ways to resolve the conflict in the framework of the negotiation process with insurgent groups. However, differences in the positions of the parties on the hard core of the problem complicate reaching consensus. The author concludes that as long as Thai society is divided into “we” and “they”, the basis for the growth of Malay nationalism remains.