Egypt, under the rule of Khedive Isma'il Pasha, first attempted to colonise the region in the 1870s, establishing the province of Equatoria in the southern portion. Egypt's first governor was Samuel Baker, commissioned in 1869, followed by Charles George Gordon in 1874 and by Emin Pasha in 1878. The Mahdist War of the 1880s destabilised the nascent province, and Equatoria ceased to exist as an Egyptian outpost in 1889. Important settlements in Equatoria included Lado, Gondokoro, Dufile and Wadelai. In 1947, British hopes to join the southern part of Sudan with Uganda were dashed by the Juba Conference, to unify northern and southern Sudan.
The region was affected by two civil wars since Sudanese independence – the Sudanese government fought the Anyanya rebel army from 1955 to 1972 in the First Sudanese Civil War and then SPLA/M in the Second Sudanese Civil War for almost twenty-one years after the founding of SPLA/M in 1983 – resulting in serious neglect, lack of infrastructural development, and major destruction and displacement. More than 2.5 million people were killed, and more than 5 million were externally displaced while others have been internally displaced, becoming refugees as a result of the civil war and war-related impacts.
On 9 January 2005, a peace treaty was signed in Nairobi, Kenya, ending the Second Sudanese Civil War and reestablishing Southern autonomy. John Garang, then leader of the Sudan People's Liberation Army/Movement, feted the treaty, predicting, "This peace agreement will change Sudan forever." The treaty provided for a referendum on South Sudanese independence to be held on 9 January 2011, six years after the original signing. It also divided oil income evenly between the North and the South
Use of sharia law continued in the Muslim-majority North, while in Southern Sudan, its authority was devolved to the elected assembly. Southern Sudan ultimately rejected implementation of sharia law. In late 2010, Sudanese President Omar al-Bashir announced that if Southern Sudan voted for independence, Sudan would fully adopt sharia as the basis for law.
President Salva Kiir Mayardit and the SPLA disputed the results of the 2008 Sudanese census, which claimed Southern Sudan accounted for 21 percent of the population. The SPLA insisted that Southern Sudan included closer to one-third of the national population and that Southern Sudanese had been undercounted.