East Africa / Horn of Africa / Sudan-South Sudan·Sudan (Southern Sudan; now Republic of South Sudan)

Second Sudanese Civil War (1983–2005)

Also known as: Sudan’s North–South Civil War (second phase); the War in the South; the SPLA War

ResolvedCivil War; Liberation War; North–South ConflictEast Africa / Horn of Africa / Sudan-South Sudan16 May 1983 – 9 January 2005 (22 years and 8 months)

SPLA, Khartoum, and the Road to Independence

Background

The Second Sudanese Civil War stands among the longest and most lethal armed conflicts in African post-colonial history. Lasting twenty-two years and costing an estimated two million lives — the vast majority civilians who died not from direct combat but from famine, disease, and displacement — it was also among the most consequential: the war ended with an agreement that eventually produced the birth of Africa’s newest state, the Republic of South Sudan, in July 2011. The conflict’s roots reached back to Sudan’s colonial era and the persistent failure to build a coherent post-independence national identity. The Anglo-Egyptian Condominium (1899–1956) administered northern and southern Sudan as effectively separate units, pursuing a Southern Policy that prioritised Christian missionary education in the south and restricted northern influence. At independence in 1956, political power concentrated in Arab-Muslim northern elites, and southern Sudan — predominantly non-Muslim, non-Arab, and significantly disadvantaged in education, infrastructure, and representation — quickly felt that independence had simply transferred colonial extraction from British to northern Sudanese hands. The First Sudanese Civil War (1955–1972) was the first armed expression of this grievance; the Addis Ababa Agreement of 1972 granted the south regional autonomy and ended that conflict. The agreement lasted only eleven years. The second war’s immediate catalyst was a decision by President Jaafar Nimeiri to systematically reverse the Addis Ababa Agreement. In 1978, Nimeiri began manoeuvring to take control of newly discovered oil fields located along the north-south border, stripping the south of the economic resource that would have funded its autonomy. On 5 June 1983, he issued Presidential Decree 1 dividing southern Sudan into three smaller regions, eliminating the unified southern authority guaranteed by the 1972 Agreement. In September 1983, Nimeiri proclaimed Sharia law across the entire country — including its predominantly non-Muslim southern population. These acts provoked a mutiny by southern troops of the 105th Battalion stationed at Bor, who fled into Ethiopia rather than face redeployment to the north. Colonel John Garang de Mabior, a southern Sudanese military officer and academic, assembled these mutineers into the Sudan People’s Liberation Army (SPLA) and its political wing, the Sudan People’s Liberation Movement (SPLM). Under Garang’s leadership, the SPLM/A was ideologically unusual: rather than calling for southern independence, Garang positioned the movement as fighting for a united, secular, democratic ‘New Sudan’ in which all Sudanese — not just the south — would have equal rights and opportunities. This framing helped the SPLM/A attract support from northern Sudanese opposition movements and gave it broader pan-Sudanese ideological credentials. However, many SPLA commanders and rank-and-file fighters were motivated less by Garang’s vision of national transformation than by a desire for southern independence or for specific ethnic group interests — a tension that would surface explosively after the CPA and help produce South Sudan’s post-independence civil war. The war proceeded through several distinct phases. From 1983 to 1989, fighting was intense but the government also engaged in sporadic peace negotiations. In June 1989, the situation transformed dramatically: Brigadier Omar Hassan al-Bashir, backed by the National Islamic Front (NIF) under Hassan al-Turabi, overthrew the elected government of Sadiq al-Mahdi in a coup that reversed tentative moves toward negotiated settlement and committed Sudan to an explicitly Islamist project. Under Bashir and Turabi, the war became simultaneously an internal conflict and a declared jihad, with the government mobilising religious framing, PDF (Popular Defence Forces) militias, and scorched-earth tactics against civilian populations in the south, the Nuba Mountains, and the Blue Nile region. August 1991 brought the conflict’s most destructive internal rupture: Riek Machar and Lam Akol attempted a coup against Garang within the SPLA, splitting the movement along broadly Nuer-Dinka ethnic lines into the original SPLA-Torit (Garang) and the SPLA-Nasir (Machar). The resulting inter-factional violence — including the Bor Massacre of November 1991 in which Nuer forces killed thousands of Dinka civilians — was among the most devastating episodes of the entire conflict and planted the ethnic seeds that would later produce South Sudan’s civil war in 2013. By 1997, a comprehensive ceasefire architecture gradually reduced inter-factional fighting, and by 2002 the path to a comprehensive agreement had opened.

Main Actors

Government of Sudan / Sudanese Armed Forces (SAF): The Khartoum-based central government, controlled from 1989 onward by the Islamist Bashir-Turabi regime. Deployed conventional military forces combined with proxy PDF militias, aerial bombardment of civilian areas, and deliberate food denial as weapons of war. Responsible for systematic atrocities against civilians in southern Sudan, the Nuba Mountains, and the Blue Nile region.
Sudan People’s Liberation Movement/Army (SPLM/A): The primary southern rebel organisation, founded May 1983. Led by Colonel (later General) John Garang de Mabior, a Dinka intellectual and soldier who articulated a ‘New Sudan’ vision of united, secular democracy rather than independence. The SPLM/A maintained bases initially in Ethiopia (until 1991) and received arms from Eritrea, Ethiopia, Uganda, and Israel. SPLM/A forces also committed atrocities and recruited child soldiers.
SPLA-Nasir / South Sudan Defence Forces (SSDF): Splinter factions led by Riek Machar (Nuer) and Lam Akol after the August 1991 coup attempt against Garang. Later coalesced under the South Sudan Defence Forces (SSDF), allied at various times with Khartoum. Responsible for the Bor Massacre (1991) and sustained inter-factional violence through the 1990s. Machar and Garang reconciled in January 2002; SSDF was largely reintegrated into the SPLA by the mid-2000s.
Government of Ethiopia (1983–1991): Under President Mengistu Haile Mariam, Ethiopia provided the SPLA with logistics, bases, and arms as part of its opposition to Khartoum. The fall of Mengistu in May 1991 forced 300,000+ SPLA-associated refugees and fighters out of Ethiopia, significantly weakening the SPLA at a critical moment and contributing to the August 1991 internal split.
Uganda: A key external backer of the SPLA from the mid-1990s. Uganda’s conflict with the Lord’s Resistance Army (LRA), which Khartoum supported as a proxy, created a shared interest with the SPLA in opposing Bashir’s regime.
Popular Defence Forces (PDF): Government-sponsored paramilitary militia, drawn primarily from northern Arab and Muslim communities, used to conduct counterinsurgency, population displacement, and scorched-earth campaigns in southern Sudan and the Nuba Mountains. Responsible for large-scale civilian atrocities.
United States, United Kingdom, Norway (the Troika) -------------------: Key international mediators in the final peace process, particularly from 2002 onward. The US Sudan Peace Act (October 2002), which accused Sudan of genocide for wartime killings in the south, created diplomatic pressure that contributed to the acceleration of negotiations. ----------------------------------------------------

Drivers

Sharia imposition and religious discrimination: Nimeiri’s September 1983 imposition of Sharia law nationwide was the most proximate trigger of the war. For the predominantly non-Muslim south, forced compliance with Islamic law — including hudud punishments — was perceived as an existential cultural and religious assault.
Oil and resource capture: The discovery of oil in the border regions between north and south in 1978 directly motivated Nimeiri’s decision to redivide the south and undermine its autonomy. Control of oil revenues remained central to the political economy of both the conflict and its eventual settlement: the CPA’s 50-50 oil revenue sharing formula was its most consequential provision.
Structural marginalisation: Decades of underinvestment in southern infrastructure, education, and public services had created severe regional inequality. The south’s exclusion from the political and economic benefits of Sudanese statehood provided the SPLM/A with a broad popular constituency.
Islamist ideological project: The Bashir-Turabi regime from 1989 onward framed the war explicitly as a jihad, recruiting fighters through religious networks, imposing Sharia in the south, and pursuing Arabisation and Islamisation policies in the Nuba Mountains and Blue Nile. This ideological dimension deepened the conflict’s intractability and international visibility.
Regional proxy dynamics: Sudan’s civil war became entangled with regional rivalries: Ethiopia and Uganda backed the SPLA; Egypt and Libya supported Khartoum; Eritrea backed the SPLA from 1993. The LRA’s use of South Sudan as a base, with Khartoum’s backing, drew Uganda deeper into the conflict. These regional dimensions both sustained the war and eventually contributed to diplomatic pressure for settlement.

Timeline

1972
Addis Ababa Agreement ends the First Sudanese Civil War (1955–1972). Grants the south regional autonomy and integrates southern fighters into the national military.
1978
Oil discovered in the border regions between north and south. Khartoum begins manoeuvring to control oil revenues, violating the spirit of the 1972 Agreement.
5 June 1983
Nimeiri issues Presidential Decree 1, redividing southern Sudan into three smaller regions and abolishing the Southern Region. Southern troops of the 105th Battalion at Bor mutiny and flee to Ethiopia.
May 1983
SPLA/M formally founded by Colonel John Garang. Initially based in Ethiopia with support from Mengistu Haile Mariam’s government.
September 198
3 Nimeiri imposes Sharia law (the September Laws) across all of Sudan, including non-Muslim southern regions. Southern resistance deepens.
6 April 1985
Nimeiri overthrown in military coup while abroad. Transitional government begins limited liberalisation. Peace negotiations begin but stall over Sharia.
1986–1988
Sadiq al-Mahdi’s civilian government negotiates with the SPLA. November 1988: SPLA and Democratic Unionist Party (DUP) reach the Sudanese Peace Initiative, calling for ceasefire and Sharia freeze. Al-Mahdi ultimately endorses it in February 1989.
30 June 1989
Brigadier Omar al-Bashir overthrows al-Mahdi’s government in an Islamist-backed coup. Hassan al-Turabi and the NIF become the power behind the regime. Peace negotiations collapse. War resumes with intensified Islamist framing.
August 1991
SPLA internal crisis: Riek Machar and Lam Akol attempt a coup against Garang. The movement splits along broadly Nuer-Dinka lines into SPLA-Torit (Garang) and SPLA-Nasir (Machar). May 1991: Ethiopia’s Mengistu falls; SPLA bases and 300,000+ refugees forced out of Ethiopia.
November 1991
Bor Massacre: Nuer forces under Machar’s SPLA-Nasir kill an estimated 2,000–2,000 Dinka civilians in Bor. Among the most severe instances of inter-factional ethnic violence in the war.
1993–1997
IGAD mediates a series of peace initiatives. Government signs separate agreements with SPLA splinter factions (Khartoum Peace Agreement, 1997). SPLA-Nasir’s Riek Machar briefly allies with Khartoum, forming the South Sudan Defence Forces (SSDF).
January 2002
Garang and Machar reconcile; the major internal SPLA split begins to close. The path to a comprehensive settlement opens.
July 2002
Machakos Protocol: SPLM/A and Government of Sudan accept the right of self-determination for southern Sudan and agree to a six-year interim period followed by a referendum. The first major breakthrough in peace negotiations.
2003–2004
Wealth-Sharing Protocol (January 2004): 50-50 split of oil revenues between GoS and Government of South Sudan. Security arrangements, power-sharing, and protocols on the Nuba Mountains, Blue Nile, and Abyei progressively negotiated under IGAD mediation.
30 July 2005
John Garang killed in a helicopter crash in Uganda’s Imatong Mountains, three weeks after being sworn in as First VP of Sudan under the CPA. A catastrophic loss for the peace process; Salva Kiir Mayardit succeeds him.
9 January 200
5 Comprehensive Peace Agreement (CPA) signed in Nairobi. Provides for a six-year Government of National Unity, 50-50 oil revenues, southern autonomy under the Government of South Sudan (GoSS) with Salva Kiir as President, and a January 2011 self-determination referendum.
9 January 201
1 Referendum on southern independence: 98.83% vote for secession. 9 July 2011: Republic of South Sudan formally declares independence, the world’s newest state.

Humanitarian Impact

The Second Sudanese Civil War produced one of the worst humanitarian catastrophes in late-twentieth-century Africa. The standard estimate of approximately two million deaths represents primarily civilian casualties from famine, epidemic disease, and displacement-related mortality rather than direct combat deaths. The UN Peace Act of 2002 accused Sudan of genocide for these wartime killings. The government’s deliberate use of food denial as a weapon of war — blocking aid convoys, raiding relief distributions, targeting agricultural infrastructure — was a primary driver of mass starvation across the south and the Nuba Mountains. Population displacement reached approximately four million at peak. Internal displacement in South Sudan, combined with large refugee populations in Uganda, Ethiopia, Kenya, Egypt, and the Central African Republic, constituted one of the largest humanitarian emergencies of the 1980s and 1990s. Children were systematically recruited as soldiers by both the SPLA and government-aligned forces; the CPA mandated demobilisation of child soldiers as a specific provision. Sexual violence, looting, and village destruction were widespread on both sides. The aerial bombardment of civilian areas by the Sudanese Armed Forces — documented by international NGOs and UN agencies — constituted systematic attacks on civilian populations.

Peace Efforts

Machakos Protocol (July 2002): The critical breakthrough: the government accepted the principle of southern self-determination and agreed to a six-year interim period. Named after the Kenyan town where it was negotiated under IGAD facilitation.
Naivasha protocols (2003–2004): A series of agreements negotiated at Naivasha, Kenya covering wealth sharing (50-50 oil revenues), power sharing, security arrangements, and protocols on the contested areas of the Nuba Mountains, Blue Nile, and Abyei. The Abyei Protocol proved most contested.
Comprehensive Peace Agreement (9 January 2005): The CPA packaged all preceding protocols into a single agreement signed in Nairobi. It created a Government of National Unity (Bashir as president, Garang as First VP), a semi-autonomous Government of South Sudan under the SPLM/A, a six-year interim period, and a January 2011 self-determination referendum. The 50-50 oil revenue split between north and south was the CPA’s economic foundation.
Unresolved issues: The CPA did not resolve Darfur (where conflict had already erupted in 2003), South Kordofan and Blue Nile (whose popular consultation provisions were never implemented), or Abyei (whose referendum was never held). These deliberate deferrals would generate subsequent conflicts.

Outlook

The Second Sudanese Civil War’s long-term impact is measured less by what it achieved than by what it produced as its aftermath. The birth of South Sudan was its most visible outcome; but South Sudan’s subsequent implosion into civil war, humanitarian catastrophe, and accelerating state failure represents the deferred costs of twenty-two years of war without genuine national reconciliation. Sudan’s own trajectory — from the CPA’s partial peace through the Sudanese Revolution to the catastrophic 2023 civil war — is equally a product of the unresolved legacies of Bashir’s misrule, which the Second Civil War both enabled and perpetuated. The war also fundamentally shaped the RSF’s genealogy. The Popular Defence Forces (PDF) mobilised by the Bashir regime for the Second Civil War in the south and the Nuba Mountains were the institutional and personnel precursor to the Janjaweed militia that conducted genocide in Darfur from 2003 and later to the RSF formalised in 2013. The weapons culture, command impunity, and ethnic violence of the PDF’s wartime campaign directly shaped the RSF’s institutional DNA.

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