Events preceding the amalgamation of the Northern and Southern protectorate of Nigeria in 1914 reveal that the North and the South were not working together as an entity. This was because the desire of the colonialists was the actualization of their imperialist policies in Nigeria through divide and rule. While the southern protectorate became more liberal in accepting the imposed cultures brought by the colonialists, the northern protectorate saw it as an attempt by the colonialists to convert the region from Muslim Communities to Christian-Western Cultures and beliefs. The resistance exhibited by the North forced the imperialists to apply in-direct rule so as to maintain a system similar to their own in the west. Southern agenda for nationhood infuriated the colonialists and made them to lower the level and quality of education of Northerners so that they did not face the same agitation for independence in the North as was the case with the South. The south was becoming more concerned with the idea of nationhood and the British administration did not want the north to have such an understanding based on Western Education. While the South was more liberal in their reasoning and understanding because of their exposure to Western education, the North had Qura’nic education and was more traditional partly due to their preference to traditional education and had similar elements with the Queen’s palace education. This motivated the colonialists to introduce policies that did not aim at bringing cohesion and integration in the North, rather policies that encouraged prejudice and animosity were developed in the region for effective imperialism as a colonial territory. The policies used for this easy imperialism included differential treatment of ethnic groups, racial and ethnic inequality and injustice, the creation of two religious communities, stratified inequality and ethnic hierarchy. Political and social alienation in effect became the bedrock for social status inequality in Nigeria particularly in Northern Nigeria. The focus of this paper therefore is to unravel this unequal treatment, trace the impact of this differential treatment and identify the basis of religious conflict in Northern Nigeria in contemporary times.