South Sudan achieved political independence in 2011, before plunging into a series of civil wars that have culminated with the signing of the Inter-Governmental Authority for Development, IGAD, driven peace agreement. The Sudan People's Liberation Movement, SPLM, Government has not created conducive environment for political stability in South Sudan. Thus, the political and economic crisis has seen the intervention of neighboring countries in internal affairs of South Sudan to pursue their national interests or within the context of regional bodies such as IGAD to achieve the same. From the outset, the independence of South Sudan was necessitated by the USA led war against global terrorism that is more pronounced at the Horn of Africa and in the context of Sudan's civil war. The natural resources in South Sudan has attracted state and non-state actors with global and regional actors directly or indirectly getting involved in reconfiguring the security matrix with diverse outcomes, some of them with unintended outcome. Wildlife trafficking, gold mining, logging, ivory poaching and illegal charcoal production and commercial bush meat poaching, has created war economics and resource conflicts within the region and beyond. Political crisis in South Sudan, especially the most recent one that triggered civil war in 2013, and persisted to date, has received very little scholarly attention especially its regional security implications. This paper seeks to analyse the security ramifications of the ongoing war for East Africa. The paper will examine the emerging security threats and their regional ramifications. In particular, multiple security ramifications such as armed groups, humanitarian crisis, natural resources and refugees' crisis will be examined in detail to draw conclusions on the scope and depth of the emerging security threats in East Africa.