This article examined the historical development of the struggle of the Muslim communities concentrated in the Southern Philippines for cultural freedom and political independence. Additionally, this study also concentrated on, on the one hand, the attempts exerted to establish an Islamic state in the Southern Philippines and Christian-Muslim competition in the country, and on the other hand, the minority policies of the Philippine governments towards the Muslim communities. In the present article, both the historical background and political fate of both Filipino Muslims were discussed, and the ethnic, socio-cultural and demographic characteristics of this country were addressed. Besides, the issue of freedom of the people of Moro and the establishment problems of Muslim Mindanao Autonomous Region and Bangsamoro Autonomous Region were examined. It is the most important consequence of this work that the peace climate between the government forces and the Muslim guerrillas in the Southern Philippines, the continuation of the social, economic, political and cultural problems of the Moro people and the independence of the Muslim communities living in the Philippine islands. Provision of the peaceful climate between the government forces and the Muslim guerrillas in the southern Philippines, the continuation of social, economic, political and cultural problems of the Moro people, and the failure of the Muslim communities living on the Philippine islands to gain their independence were the most important results of this study.