This paper examines the Impacts of colonization Towards Muslim Communities in the Philippine Islands; it will clarify the first inhabitants and Native Peoples of the Philippine Islands before the coming of Christian colonizers. The tendency of giving priority to discuss the impacts of colonization Towards Muslim Communities in the Philippines as a study analysis is to clarify and trace the Hidden History of the Muslim Filipinos. To address this limitation, an analytical study is conceived to foreground the impacts of colonization towards Muslim Filipino and to show the colonial's method of Liquidating Islamic Religion in the Philippines by Christian colonizers. The objectives of this study are to identify and trace the first settlers who came first to the Visayas and Luzun and to show the first Rajahs or Kings in the Philippines Islands before the coming of Spaniard and American colonials, and to show the real history of the Philippine Islands. Discourse Analysis will use in this study in order to identify the impacts of colonizatio, contextualizing and examining, synthesizing and understanding/confirming/clarifying the reality of the Impacts of colonization Towards Muslim Filipino communities. The study single out first; that the Impacts of colonization towards Muslim Communities in the Philippines are no contradictory between the Muslim Filipinos about its impacts. At the end, the study gives the clear framework of the impacts of the colonization towards Muslim Filipino communities all over the Philippines.