South Sudan gained independence in 2011 after a much applauded referendum. The euphoria of this accomplishment was beclouded by ethnic conflicts which degenerated into a civil war in December 2013. The aim of this study was to examine the conflict that degenerated into a civil war in South Sudan and orchestrated gruesome sexual violence. In accordance, the study was guided by the following research questions. Why is the civil war in South Sudan said to be an ethnic conflict? How is sexual violence manifesting in the conflict of South Sudan? The instrumentalist theory of ethnic conflict as propounded by Pierre Duhem was adopted as the theoretical framework of this study. The research employed a qualitative method of study. The study found out that South Sudan is a composition of more than 60 ethnic groups but the Dinka, Nuer and to a lesser degree the Murle are the most prominent. Incidentally, the conflicts that have engulfed and devastated all of South Sudan emanated and proliferated from these major ethnic groups. The conflict in South Sudan was characterized by sexual violence such as rape, sexual slavery, sexual torture, sexual mutilation etc. The study concludes that ethnicity is the fundamental causal factor of the conflict of South Sudan that is characterized by sexual violence and other atrocities. The study recommends that South Sudan should harness its rich national heritage of multi-ethnicity for unity in diversity as opposed to the prevailing parochial barbarity of ethnic conflicts.