South Sudan’s administrative boundaries stem from the colonial period. Since it gained independence in 2011, subsequent rounds of reshuffling of the political system, internal borders, and power relations have been a source of confusion, elite manipulation, and conflict throughout the country. This paper explores the impact of this confusion by focusing on multiple shifting linkages between administrative boundaries and identities and shows how the mobilization of ethnic identities has become central to territorial claims and creating territorial borders. We use three local conflicts in Central Equatoria State to illustrate how claims of belonging and entitlement are being used by elites for economic, political, and socio-cultural gains. The three cases also show how such manipulation increases the likelihood of ethnic division and conflict. Following the decision by the government in 2015 to increase the number of states from 10 to 28 in October 2015, further manipulation of borders and identities is likely to occur and could result in more violence, ethnic-based conflict, and human suffering.