There is general consensus that contemporary African conflicts are fueled by the need to protect identity and are based on ethnicity, religion or the combination of the both. These conflicts start as latent with identity structural causes and if not resolved they have most often turned violent and protracted becoming more difficult to resolve. To this end, this study explored implications of religion intolerance on state security in Africa using Malawi as a case study, Lilongwe City to be specific. The study was anchored on Social Identity Theory which argues that groups or individuals dedicate themselves in protecting what they believe is in the best interest of the group to protect or further group identity. The study was more qualitative though some quantitative techniques were also incorporated. Apart from using secondary data, primary data was collected using questionnaire. Analysis involved content analysis for qualitative data and quantitative data was analyzed using Microsoft Excel software.Key findings of this study are that intolerance in Malawi is existent and is increasing over time with waves of violent events, thus negatively affecting state security. The policies and strategies in place now are less effective while some policies and strategies which could have been useful are non-existent. Resource constraints and contradicting irreconcilable beliefs are among some of the obstacles to effective implementation of the available policies and strategies. Uses of coercive measures to address religious intolerance have not been effective because they only address the surface while underlying causes remain intact. On the other hand, faith-based organizations have proved to be useful in addressing such issues. Overall, the study recommends that Malawi government; explore proactive measures that would address religious conflicts in their latent stages using noncoercive strategies and policies. The government should also provide sufficient resources for effective implementation of available policies and strategies. At the same time there is a need to fast track drafting new policies to cover gaps exposed by this study.

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