Following Riek Machar’s return to Juba in April and the formation of a transitional government, marked the most significant milestone of the August 2015 Agreement on the Resolution of the Conflict in the Republic of South Sudan (ARCSS) that ended the twenty-month civil war. Though, the ARCSS, designed to address a war primarily fought between the government and the Sudan People’s Liberation Movement/Army-In Opposition (SPLM/A-IO) in the Greater Upper Nile region, is an imperfect solution to other conflict fault lines, notably in the Equatoria region. Conflicts there are driven by a combination of national governance issues – federalism, security sector reform and a new constitution – that the ARCSS addresses – and localised grievances. Though the Equatorian conflicts appear to be on the wane, the agreement’s ability to address national political and security governance issues as well as regional specific questions about the status of Equatorian opposition forces will determine if they revive. This report provides a brief political and conflict history of the Equatorias. It identifies the stresses the recent civil war put on the region and the path from local insurrection into open rebellion in parts of Western Equatoria. It concludes with a discussion of the relationship between these conflicts and the ARCSS and peace prospects under the transitional government. Appendices below on the SPLA and key armed groups identify their areas of operations, structure, leadership and prospects.