This article tries to figure out the influence of the wide spread Islamic resurgence movement on the Philippine muslim community, and more specifically on the effects given to the development of the separatist movement in the Philippine Mindanao. The muslim separatist movement in the Philippines is an outcome of the communal sense of marginalization and deprivation resulting from the modernization process led by the central government ever since the independence. However, the more fundamental energy, which made possible to outbreak the separatist movement, could be found in the Islamic resurgence movement that slipped into the Philippines during the earlier days. The Islamic resurgence movements in the Philippine Mindanao was characterized by the missionary works and education activities, and these activities created an unified Islamic national identity, so-called Moro nationalism, among the traditionally divided Philippine muslim community. Based on the unified identity Philippine muslims strive to establish an independent Islamic state, and ceaselessly engage in conflicts with the central government. Despite the continuous negotiations and compromises during the past 50 years, the conflict has not come to an end until today. The reason could be found in the weak central government power to handle communal conflicts, the continuous breakup of the muslim power block, and the half-hearted and short-sighted arbitration of the third party. Unless the three factors remain constant, the conflict of identity in the Philippine Mindanao would be continued.