The purpose of this dissertation is to present an exposition and Christian ethical evaluation of the violent conflict in Southern Philippines between the Bangsamoro people and the Armed Forces of the Philippines (AFP) representing the central government of the Republic of the Philippines (GRP). The Bangsamoro people, the original Muslim inhabitants of Mindanao at the time of colonization by the Spanish in 1521, now comprise only about five per cent of the total 90 million Philippine population. The Bangsamoro people have been at war with the Christian dominated government since the 1960‘s. Their struggle is for self-determination within their ancestral homeland in Mindanao. They consider self determination as a way for them to uphold and enrich their Muslim cultural heritage, religion, and identity. It is equally an expression of their desire to recover their pre-Spanish period (1521) of political and economic authority in the Southern Philippines. They are not asking for the whole of the region of Mindanao, but want a parcel of it, especially where they predominate. This will enable generations after them to live in peace and piety, as Islam enjoins all believers. The organised Muslim armed revolt against the Armed Forces of the Philippines has dragged on for almost forty years. This dissertation examines and ethically evaluates this conflict in the context of past Spanish and American colonialism. It is understood in this dissertation as an identity conflict, and religion is considered as a distinctive feature of each combatant group. However, in the light of the events of 9/11 and terrorist atrocities in Bali, Barcelona, London and India, and the wars in Iraq and Afghanistan, including tensions in Palestine, the conflict in Mindanao has taken on a religious hue.