The article examines the history of the development of the nationalist movement of Malay Muslims living inthe south of Thailand, which is more thanhalf a century old and is a demonstrationof their identify in conditions of being inan alien and even hostile religious, cultural and ethnic environment and a form ofprotest against the government policy offorced assimilation. The desire of MalayMuslims 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 anideology of ethno-nationalism and as a political movement of Malay Muslims, whichoriginated in the 1940s of the last century, has transformed in the last fifteen yearsinto a religious jihad with an accompanying increase in violence. It is based onsmall groups of militant separatists recruiting their supporters from studentsof traditional Muslim schools. Having almost completely abandoned political activity, the separatists concentrated on carrying out acts of terror. With the emergenceof ISIS and its attempts to create its basein the Muslim countries of Southeast Asia,a threat arose that a local conflict woulddevelop into a transnational one. However, local jihadists, following the interests ofself-survival and adhering to a nationalist ideology, show their distance from ISIS,avoiding involvement in the internationalterrorist movement. The author notes thatdespite the limited social base of terroristseparatist groups, the idea of independenceremains widely demanded in local society. The prolonged nature of the ethno-religious conflict poses the task to resolve it byThai government. Attempts to suppress theseparatism of Malay Muslims by force havebeen unsuccessful, which prompts the Thaigovernment to look for political ways to resolve the conflict in the framework of thenegotiation process with insurgent groups.However, differences in the positions of theparties on the hard core of the problemcomplicate reaching consensus. The authorconcludes that as long as Thai society is divided into “we” and “they”, the basis for thegrowth of Malay nationalism remains.