This dissertation is about the ethnicity and war on Christian-Muslim Relations among South Sudanese in Nairobi. The two religions, Christianity and Islam has been the main focus in both Sudans, but currently, ethnicity has taken shape among south Sudanese in the Diaspora. The motivation based on ethnic and war involvement in the South has impacted on religious, political, economic, cultural and social relations base on perception. The purpose of this dissertation was to investigate how the ethnicity and war has affected Christian-Muslim relations among South Sudanese refugees in Nairobi. This thesis was to inform how Christian-Muslim relations have been affected by ethnicity and war, not only on religions, but also on political, economic, social and cultural factors. The elites used ethnicity as a way to mobilize common citizenry for their success on ethnic war. The issue of religions in South Sudan is now irrelevant in this ethnic war, religion has now suffered and it is in dilemma because of ethnic ability to wage identity among South Sudanese. The current war is not like the former war with Northerners where religion took center stage between the South and the North. Ethnicity in the South has shaped the minds of people and their identity based on where you came from. The perception and lack of trust among South Sudanese put Christianity and Islam in question and makes religion being subordinate by ethnic values within South Sudanese in Nairobi. The solution to this ethnic war is to allow people to dialogue their values and norms among themselves, and for them to create the space of Christianity and Islam in diaspora.