On 18 August 1955, members of the British-administered Sudan Defence Force Equatorial Corps mutinied in Torit, and in the following days in Juba, Yei, and Maridi.
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.
In 1969, Gordon Muortat Mayen was elected unanimously as the new leader of the South. Southern Sudan in this time changed their name to the Nile Republic and resumed warfare against Khartoum, however some of the former leader Jaden's troops would not accept a Dinka leader and fought against the Anyanya.
The South was first led by the late leader Aggrey Jaden; he left the movement in 1969 due to internal political disputes.
After a second military coup on 25 May 1969, Col. Gaafar Nimeiry became Prime Minister and promptly outlawed political parties.
In 1971, former army lieutenant Joseph Lagu formed a successful coup d'état against Gordon Muortat with help from Israel, which pledged him their support. He then gathered all the guerilla bands under his Southern Sudan Liberation Movement (SSLM).
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.
Mediation between the World Council of Churches (WCC) and the All Africa 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.