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This paper updates the now well-known work of scholar Douglas Johnson on the political ecology of the Greater Upper Nile region of South Sudan. Johnson’s 1989 work, Political ecology in the Upper Nile: the twentieth century expansion of the pastoral common economy in the Journal of African History contributed to the emergence of the now prominent political ecology approach. This work brings this work forward to include the recent civil war in South Sudan and the associated politics of peace. Through this approach we can see the relationship between the environment, the communities and the conflict continue to hold explanatory value. It is increasingly an important perspective for the practice of peacebuilding. The paper engages the current issues of the management of the Nile, development challenges, as well as how the emerging South Sudanese state is attempting to shape a region that har rejected myriad efforts at control and governance. Most notably has been the return of the discussion of the Jonglei Canal, one of the impetuses of Sudan’s Second Civil war. Amidst the current politics of the region, the political ecology of Greater Upper Nile also sheds light on the regional political and international security situation.