The secessionist conflict in southern Philippines erupted in the 1970s to assert Muslim self-determination and establish a Bangsamoro state. Despite the government's peace efforts, the conflict persisted for more than four decades, causing instability and hindering progress in the region. For centuries, Muslim sultanates had dominated and ruled Mindanao and Sulu based on Islamic laws and practices. However, colonization and post-colonial influence significantly altered the Muslims' distinct identity as a dominant ethno-religious group of people. Notwithstanding strong Muslim resistance, colonial and post-colonial rule prevailed and eventually transformed the Muslims into the minoritized group in Mindanao. This study looked into the impact of colonial and post-colonial land ownership and migration policies on the rise of Muslim secessionist conflict, and found that Muslims were discriminated against, marginalized, and dispossessed of their ancestral lands and domination in Mindanao. Muslim resentments and grievances that developed over time fueled the rise of the contemporary secessionist conflict in Mindanao. Moro ancestral domain and territory were vital and contentious issues in the efforts to settle the secessionist conflict. Deeper understanding of the complexities of this problem is a key to attaining a viable solution for a lasting settlement of the Muslim conflict in Mindanao.