In 1983, President of Sudan Gaafar Nimeiry declared all Sudan an Islamic state under Shari'a law, including the non-Islamic majority southern region. The Southern Sudan Autonomous Region was abolished on 5 जून 1983, ending the Addis Ababa Agreement. In direct response to this, the Sudan People's Liberation Army/Movement (SPLA/M) was formed under the leadership of John Garang, and the Second Sudanese Civil War erupted. Several factions split from the SPLA often along ethnic lines and were funded and armed by Khartoum, with the most notable being the SPLA-Nasir in 1991 led by Riek Machar.

As a result of the infighting, more southerners died at each other's hands than were killed by northerners during the war. In the Bor massacre in 1991, an estimated 2000 civilians were killed by SPLA-Nasir and armed Nuer civilians and another estimated 25,000 died from the resulting famine in the following years. This war lasted for twenty-two years (until 2005), becoming the longest civil war in Africa.

In 2005, Comprehensive Peace Agreement, mediated by the Intergovernmental Authority on Development (IGAD), as well as IGAD-Partners, a consortium of donor countries, was signed in Nairobi and autonomous Government of Southern Sudan was formed. This agreement lasted until 2011, when South Sudan declared independence.

Republic of Sudan
Egyptian conquest under the Muhammad Ali Dynasty
Second civil war
Tribal conflict