Nigeria

Ongoing and sporadic low-level conflict between northern Muslims and southern Christians, also involving indigenous 'animist' faiths.
 
This conflict originates in the colonial formation of Nigeria, which overrode tribal and cultural territories, forcing diverse African nations and cultures into an incompatible union based mainly on colonial priorities. This gave the christianised coastal peoples such as the Yoruba dominance over more northerly Muslim Nilotic peoples or the southern Ibo (which gave rise to the 1960s Biafra War).
 
More recently, Northern Muslims (such as the Hausa), empowered by the Muslim revival from the 1980s onwards, have increasingly opposed southern Christian (Yoruba) dominance and the secular military regimes of recent decades, seeking to institute sharia law or variations of it in some states. This has also involved Muslim opposition to traditional indigenous faiths. Amongst Christians, indigenous ways have more readily blended into Christian beliefs.
 
Mostly civil unrest. 14,000 dead since 1999, 200,000 displaced. Disturbances in 2008, such as in the city of Jos, have killed hundreds, causing many to lose their homes. The main causes of conflict are ethnic and political, amped up by economic exclusion and corruption, though social and national divisions polarise along religious lines, mainly north-south.
 

Links:

Reuters Alernet: Nigerian Violence
Wikipedia: Religion in Nigeria
Global Security: Nigeria