The Sudanese conflict in South Kordofan and Blue Nile was an armed conflict and insurgency in the Sudanese states of South Kordofan and Blue Nile (known as the Two Areas) between the Sudanese Armed Forces (SAF) and the Sudan People's Liberation Movement–North (SPLM-N), a northern offshoot of the Sudan People's Liberation Movement (SPLM) in now neighbouring South Sudan. After some years of relative calm following the 2005 agreement which ended the Second Sudanese Civil War between the Sudanese government and SPLM rebels, fighting broke out again in the lead-up to South Sudan's independence on 9 July 2011, starting in South Kordofan on 5 June and spreading to the neighboring Blue Nile state in September. SPLM-N, splitting from newly independent SPLM, took up arms against the retained inclusion of the two southern states in Sudan with no popular consultation and against the lack of democratic elections. The conflict is intertwined with the War in Darfur, since in November 2011 SPLM-N established a loose alliance with Darfuri rebels, called Sudan Revolutionary Front (SRF).

As of October 2014, some two million people have been affected by the conflict, with more than 500,000 having been displaced and about 250,000 of them fleeing to South Sudan and Ethiopia. In January 2015, fighting intensified as Omar al-Bashir's government tried to regain control of rebel-held territory ahead of April 2015 general elections.

With the overthrow of al-Bashir in April 2019 following months of protests, the SRF announced a three-month ceasefire, hoping to facilitate a Sudanese transition to democracy. This led to the beginning of peace negotiations between the rebels and the new interim government. The Sudanese peace process was formalised with the August 2019 Draft Constitutional Declaration, signed by military and civilian representatives during the Sudanese Revolution, that mandates that a peace agreement be made in South Kordofan and Blue Nile (and in Darfur) within the first six months of the 39-month transition period to democratic civilian government.

On 31 August 2020, a comprehensive peace agreement was signed in Juba, South Sudan, between the Sudan's transitional government and the Sudan Revolutionary Front. The Sudan People's Liberation Movement-North led by Abdelaziz al-Hilu and Sudan Liberation Movement/Army led by Abdul Wahid al-Nur refused to sign the agreement.

An agreement was reached between the transitional government and the SPLM-North al-Hilu rebel faction on 3 September 2020 in Addis Ababa to separate religion and state and not discriminate against anyone's ethnicity in order to secure the equal treatment of all citizens of Sudan. The declaration of principles stated that “Sudan is a multi-racial, multi-ethnic, multi-religious and multi-cultural society. Full recognition and accommodation of these diversities must be affirmed. (...) The state shall not establish an official religion. No citizen shall be discriminated against based on their religion.”

Background

Although South Kordofan and Blue Nile are north of the Sudan–South Sudan border, many of their residents (particularly in the Nuba Mountains) identify with South Sudan with many of them having fought alongside the southern rebels during the Second Sudanese Civil War.

South Kordofan and Blue Nile were not allowed to participate in the January 2011 referendum to create South Sudan, and the "popular consultation" process they were promised also failed to take place.

According to satellite imagery, during early spring 2011, Sudan elevated dirt roads needed for tank transportation and in March 2011 it started deploying police and military installations in the area.

May 2011 Abyei conflict In May 2011, ahead of South Sudan's scheduled independence, tensions rose around the status of the Abyei Area, an oil-rich region that was statutorily part of both South Kordofan and Northern Bahr el Ghazal states. As South Kordofan was slated to remain with Sudan while Northern Bahr el Ghazal was seceding together with the rest of what was then Southern Sudan Autonomous Region, the status of Abyei was unclear, and both Khartoum and Juba claimed the area as their own.

On 19 May 2011, militants reportedly affiliated with the Sudan People's Liberation Army attacked a convoy of mixed Sudanese Army and UNMIS vehicles 10 km north of Abyei town as they withdrew from the area's administrative centre, drawing condemnation from both the Sudanese government and the United Nations.

At least 15 Sudanese tanks entered Abyei town on 20 May, beginning large-scale fighting in Abyei. By 22 May, the Sudanese military had seized control of the town, and most of Abyei's residents had fled south toward Bahr el Ghazal. Both the Sudanese government and the government of Southern Sudan accused one another of violating the terms of the Comprehensive Peace Agreement.

In June 2011, an African Union panel headed by former South African president Thabo Mbeki tried to de-escalate the situation through north–south talks in the Ethiopian capital Addis Ababa. On 20 June, the parties agreed to demilitarize the contested area of Abyei, and UN peacekeepers were deployed as part of United Nations Interim Security Force for Abyei on 27 June. The agreement details how a new Abyei administration council would replace the one dissolved by president Omar al-Bashir in May 2011. Its chief shall be picked by the SPLM but must be approved by the northern National Congress Party (NCP). The deputy however, would be nominated by the NCP and endorsed by SPLM. Three of the five heads of the departments of the administrative council would be nominated by the SPLM and the remaining two by the NCP. A police service would be established for the region, with the size and composition determined by a joint committee co-chaired by northern and southern officials. The US Secretary of State Hillary Clinton and United Nations Secretary-General Ban Ki-moon welcomed the accord but said the real test would be how both sides would implement the deal.

On 21 June, a statement was attributed to the NCP's official in charge of the Abyei file, Didiri Mohamed Ahmed, as saying that there was an understanding reached at the Addis Ababa meeting between the two parties that South Sudan would concede future ownership of Abyei to Sudan. However, the spokesman of SPLA, Philip Aguer, told the press that the statement from the NCP senior official was incorrect.

Conflict in South Kordofan and Blue Nile 2011

June On 5 June 2011, armed conflict broke out between the government of Sudan and the Sudan People's Liberation Movement–North (SPLM–N) in South Kordofan, ahead of the scheduled independence of southern Sudan on 9 July. The Sudanese Army said that the SPLA launched an attack on a police station and stole weapons prompting a response. The SPLA claimed that the Sudanese Army attempted to disarm their units by force. That day, the Justice and Equality Movement (JEM) rebel group claimed to have destroyed an army camp in the area of Jama, South Kordofan, killing 38 soldiers and wounding other 27.

On 14 June, the UN accused the Sudanese government of carrying out an "intensive bombing campaign" near the north–south border which has led to "huge suffering" for civilians in South Kordofan. Some 140,000 people fled the fighting. Aid agency offices were looted, churches were ransacked and buildings destroyed. Aid workers said that ethnic Nubans are being targeted by the Sudanese Army and Arab militias. This was denied by Rabbie Abdelattif Ebaid, an adviser to Sudan's information minister, who said that only rebel fighters were being targeted.

On 15 June, US President Barack Obama called for a ceasefire urging both the north and south to "live up to their responsibilities" to prevent a return to civil war. The head of the Anglican church, Archbishop of Canterbury Rowan Williams said: "The humanitarian challenge is already great, and the risk of another Darfur situation, with civilian populations at the mercy of government-supported terror, is a real one".

On 19 June, Sudanese president Omar al-Bashir accused the SPLM-N of "betrayal" in South Kordofan. "If they want war...we will show them practically like what happened in Abyei and South Kordofan" Bashir said. "It is better that they [SPLM-N] come to us in good terms and we will be better than them," he added. The Sudanese Army said that it would continue its military campaign in South Kordofan, which included aerial bombardment, until it crushes the rebellion led by former deputy governor and leading SPLM-N figure Abdelaziz al-Hilu. Fighting intensified around the state capital of Kadugli.

July–August On 6 July a JEM field commander announced that his forces were able to defeat an army battalion in a field near Heglig, comprising fifty four members, arranged a trap for the army battalion, which was composed of nine Land Cruisers. The head of the battalion was killed, along with two other soldiers.

On 11 July, clashes were reported in Fula, South Kordofan. Sudanese Federal National Front claimed that their forces killed 20 Sudanese soldiers, and destroyed four of the seven Land Cruisers, that carried the Sudanese soldiers. Their spokesman said that they also seized fire arms and ammunition. The remainder of the government troops fled.

Fighting continued after South Sudan gained independence on 9 July, though the Sudanese government insisted that order had been restored in South Kordofan.

A UN report leaked on 18 July documented alleged war crimes in South Kordofan, claiming that both sides targeted civilians but that the Sudanese government did so more severely with them being accused of "forced disappearances, targeting of UN staff and summary executions." The following day, UN Undersecretary-General for Humanitarian Affairs Valerie Amos called for an independent investigation into atrocities possibly committed during the conflict. Amos said the Government of Sudan should lift its restrictions on access to the region.

Joint SPLM-N and JEM forces defeated government forces from 10 to 17 July in the Nuba Mountains. An army garrison in Al-Tais was captured by rebels. By the end, 150 government soldiers and 1 rebel were killed, considerable amounts of weaponry including light and heavy machine guns and artillery, RBJ, AK47 and anti air craft missiles were captured by rebels. Also 3 rebels were captured.

It was reported on 27 August that a JEM leader had been captured and sentenced to death by hanging. Around the same time, the Sudan Tribune reported that the SPLM-N, the JEM, and the Sudan Liberation Movement (SLM) had formed a tentative alliance to resist the federal government in Khartoum.

September–December On 1 September, SPLM-N rebels in South Kordofan claimed the military was deliberately destroying crops and farms belonging to the Nuba people in an attempt to starve the state into submission. Meanwhile, state-run media claimed SPLM-N guerrillas killed 17 civilians, including children, and wounded 14 in the Kalugi region of South Kordofan on the same day.

On 7 September, clashes between Abdel Wahid's Sudan Liberation Army and the Sudanese army were reported in Jebel Marra. Rebels claimed to have killed 40 Sudanese soldiers and captured six of their vehicles. Three rebels were killed and another four were wounded.