The Shari’ah controversy is an issue that is burning in the hearts of many Nigerians, as they express their opinions in books, newspapers, magazines, Mosques, Churches and many other sources of disseminating ideas and beliefs. Most Christians seem to be antagonists and viewed Muslims as protagonists of Shari’ah through their opinions. This has a negative impact on Muslim-Christian relations and peaceful co-existence in the country. The Shari’ah in Nigeria has a long history dating back to the fifteenth century when Rumfa, the Emir of Kano introduced it and the Mais of Borno (Emperors of Borno Empire) institutionalized Islam as state religion with Shari’ah as a legal code. This study examines the controversies over the implementation of Shari’ah legal system and how the issue of Shari’ah affects MuslimChristian relations and peaceful co-existence in Nigeria. The paper begins with conceptual discussion about Shari’ah. This is followed by an account of the history of Shari’ah in Nigeria, colonialism and Shari’ah as well as the bases for Christians‟ antipathy of Shari’ah implementation in Nigeria. The paper also discusses the impact of Christian perception of Shari’ah on Muslim-Christian relations and finally makes a conclusion.