After the February 1953 agreement by the United Kingdom and Egypt to grant independence to Sudan, the internal tensions over the nature of the relationship of north to south were heightened. Matters reached a head as the 1 January 1956 independence day approached, as it appeared that northern leaders were backing away from commitments to create a federal government that would give the south substantial autonomy.
However, the insurgents gradually developed into a secessionist movement composed of the 1955 mutineers and southern students. These groups formed the Anyanya guerrilla army. (Anyanya is also known as Anyanya 1 in comparison to Anyanya 2, began with the 1974 mutiny of the military garrison in Akobo.) Starting from Equatoria, between 1963 and 1969 Anyanya spread throughout the other two southern provinces: Upper Nile and Bahr al Ghazal. However, the separatist movement was crippled by internal ethnic divisions.
The government was unable to take advantage of rebel weaknesses because of their own factionalism and instability. The first independent government of Sudan, led by Prime Minister Ismail al-Azhari, was quickly replaced by a stalemated coalition of various conservative forces, which was in turn overthrown in the coup d'état of Chief of Staff Lt. Gen. Ibrahim Abboud in 1958. Resentment at the military government led to a wave of popular protests that led to the creation of an interim government in October 1964. These protests were the first appearance of Islamist Hassan al-Turabi, who was then a student leader. Between 1966 and 1969, a series of Islamist-dominated administrations proved unable to deal with the variety of ethnic, economic and conflict problems afflicting the country. After a second military coup on 25 May 1969, Col. Gaafar Nimeiry became Prime Minister and promptly outlawed political parties. In-fighting between Marxist and non-Marxist factions in the ruling military class led to another coup in July 1971 and a short-lived administration by the Sudanese Communist Party before anti-Communist factions put Nimeiry back in control of the country.
In 1971, former army lieutenant Joseph Lagu gathered all the guerilla bands under his Southern Sudan Liberation Movement (SSLM). This was the first time in the history of the war that the separatist movement had a unified command structure to fulfill the objectives of secession and the formation of an independent state in South Sudan. It was also the first organization that could claim to speak for, and negotiate on behalf of, the entire south. Mediation between the World Council of Churches (WCC) and the All African Conference of Churches (AACC), both of which spent years building up trust with the two combatants, eventually led to the Addis Ababa Agreement of March 1972 ending the conflict. In exchange for ending their armed uprising, southerners were granted a single southern administrative region with various defined powers.