The 21-year civil war between north and south Sudan officially ended in 2005 but tensions remain between Khartoum and South Sudan, which seceded in July 2011.
Despite a lengthy peace process, negotiations have so far failed to resolve some key issues.
Both Khartoum and South Sudan are heavily dependent on oil revenues, and the division of oil wealth is still under discussion. Three-quarters of oil is in South Sudan, but all the infrastructure to export it (pipelines, refineries and Red Sea port) is in the north. Khartoum has lost a lot of revenue from oil since the split.
In January 2012, the dispute over oil reached a crisis point. South Sudan shut down its oil production in protest after Khartoum started to seize some southern crude to compensate for what it called unpaid transit fees.
The two sides agreed in March 2013 to resume oil flows, but in June Sudan said it would stop South Sudan’s crude exports unless Juba gave up support for insurgents operating across their border. Sudan and South Sudan regularly trade accusations of supporting insurgencies on each other's territory. Both sides deny supporting rebel groups.
The demarcation of the 2,000 kilometre north-south border is another contentious issue.
In 2012, both sides agreed to form a demilitarized buffer zone, to be monitored by joint border security teams. This has not yet been implemented.
Three oil-rich border states, together called the Three Areas, are potential flashpoints between the two countries and there has been a build-up of forces and arms in all three states.
For more on the north-south civil war, see Thomson Reuters Foundation's South Sudan briefing.
Oil-rich Abyei, South Kordofan and Blue Nile states lie along the border between Sudan and South Sudan, and are home to many people who fought alongside southern rebels during the civil war.
Major clashes in all three states between pro-Khartoum and pro-Juba forces have led hundreds of thousands to flee their homes.
Abyei is claimed by both countries, while South Kordofan and Blue Nile lie in Sudan.
Abyei’s status is unresolved. A referendum over whether it will join the north or the south was promised under the 2005 peace deal, and was meant to have taken place in January 2011, but the two governments could not agree the terms of the vote.
Khartoum insists that the Missiriya – seasonal migrants who graze their cattle in Abyei during the dry season – must participate, but Juba says the Ngok Dinka – Abyei’s main residents – must decide the future of the territory.
The pro-Khartoum Missiriya – some of whom fought as proxy militias in the civil war – have threatened war if they are not given ballots in the referendum. They fear they will lose grazing rights and their livelihoods if an international border runs through their grazing land, even though these rights are enshrined in the 2005 peace deal.
The Ngok Dinka want Abyei to join South Sudan.
The state has seen several outbreaks of fighting between northern and southern troops since 2005.
In May 2008 clashes displaced tens of thousands and re-ignited fears of a new civil war between north and south Sudan. After that, joint north-south forces began operating in the region. In July 2009, both sides said they accepted a ruling by an independent arbitration court in The Hague over Abyei's borders, placing the major Hejlij oil fields outside Abyei and leaving huge tracts of fertile land inside Abyei.
The Missiriya rejected the ruling, saying they had not been properly consulted. Their rejection meant the border was not demarcated.
Violence worsened in 2011, when a series of clashes between Khartoum-backed militias and south-linked groups and a build-up of government troops from both sides culminated in a full-scale military takeover by Sudanese forces in May. About a third of civilian structures were razed in Abyei town, according to the Satellite Sentinel Project. Around 110,000 people – mostly Ngok Dinka residents – fled the area.
The following month, north and south agreed to demilitarize Abyei and allow U.N. troops to monitor the peace. They also agreed to the appointment of a new Abyei administration, which had been unilaterally dissolved by Sudan in May.
The United Nations established a new peacekeeping force, the United Nations Interim Security Force for Abyei (UNISFA), consisting of 4,000 Ethiopian troops.
But for months the UNISFA troops guarded an area almost empty of inhabitants – the majority of Ngok Dinka did not return, and Khartoum’s forces remained in Abyei.
In March 2012, fighting broke out around the disputed Hejlij area. South Sudan forces and fighters from the Justice and Equality Movement – Darfur’s main rebel group – briefly took possession of the oil-rich area, forcing out the Sudanese army. South Sudan said the occupation of the disputed area could not be a violation of Sudanese sovereignty because its status was still unresolved.
A U.N. resolution in May called for an immediate end to fighting between the two countries, and demanded that both sides withdraw all their forces from Abyei. South Sudan withdrew its police force, and Sudan withdrew most of its troops but kept in place a small force surrounding Defra, Abyei’s only remaining oil field.
The Ngok Dinka have been returning to the territory, but slowly. The area still lacks an administration, and its status is still unresolved.
The situation deteriorated in May 2013 when armed Missiriya killed the leader of the Ngok Dinka in Abyei, Kuwal Deng Mayok.
The Ngok Dinka held a one-sided, symbolic referendum in October 2013 in which they voted to join South Sudan. The Misseriya did not take part, and the results have not been recognised by Juba, Khartoum or the African Union.
South Kordofan lies in north Sudan, along the disputed border with South Sudan. It is home to the most productive oil fields under Khartoum's control.
Many in the state sided with the southern rebels during the civil war, and feel betrayed by the 2005 peace deal which put the state under Khartoum's control.
In the 1980s local discontent at political marginalisation drove many Nuba to sympathise with the southern rebels.
The Nuba are people from several black African tribes, and have distinct languages and culture which clashed with the government's Arabist policies and conservative brand of political Islam. Some Nuba are Muslims, others are Christians or animists.
Khartoum responded by arming Arab-majority militias.
In 1992, the governor of Southern Kordofan formally declared a jihad – or holy war – in the Nuba Mountains. According to Foreign Policy, the campaign included the use of chemical weapons against civilians, starvation, murder, rape, enslavement and land seizure.
Hundreds of thousands of Nuba were forcibly displaced, and as many as 200,000 people died. The north's forces targeted Muslims, as well as Christians and animists.
Unlike Abyei, the 2005 peace deal that ended the civil war did not give the people of South Kordofan the right to choose whether to join the north or south.
Many Nuba are demanding political reform and autonomy and thousands still serve in a rebel armed force, the Sudan People's Liberation Movement-North (SPLM-N). The SPLM was a major rebel group during the north-south civil war, and is now the ruling party in South Sudan. It denies supporting SPLM-N rebels across the border.
Tensions in South Kordofan rose following the state's May 2011 governorship elections, with SPLM-N saying it had been cheated of victory. Sudan's ruling National Congress Party candidate Ahmed Haroun – who is wanted by the International Criminal Court for alleged war crimes in Darfur – was declared winner and soon afterwards former SPLM fighters were ordered to disarm.
In early June 2011, fighting broke out in the state capital, Kadugli, between SPLM rebels and the northern army supported by Khartoum-backed militias. The SPLM in rural Nuba Mountains quickly consolidated control over its areas, according to Small Arms Survey.
"We are facing the nightmare of genocide of our people in a final attempt to erase our culture and society from the face of the earth," said the Episcopal Bishop of Kadugli and the Nuba Mountains, Andudu Adam el-Nail.
Khartoum accused the rebels of launching an uprising to try to seize control of the state ahead of South Sudan's July 9, 2011 secession.
Hundreds of thousands of civilians have been forced to flee aerial bombardment and ground attacks, according to U.N. reports. Many have sought refuge in South Sudan or other parts of Sudan.
The SPLM-N managed to seize more territory and weapons than they ever had during the war of 1985 to 2005, International Crisis Group (ICG) said.
Sudanese government troops and Khartoum-backed Arab militias have targeted Nuba civilians, carrying out bombing campaigns and going house to house killing people, Human Rights Watch said. Khartoum has denied the allegations.
There have also been reports of Sudan bombing refugee camps in South Sudan where many have sought shelter.
Misseriya Arabs – who fought for the government during the first war – are frustrated with Khartoum, especially its 2005 decision to abolish West Kordofan, the state that represented the tribe’s ethnically homogenous homeland. They no longer heed the government’s calls to remobilise, and many young Misseriya have joined the SPLM-N, International Crisis Group says.
In early 2013, people began returning to government-controlled areas, as security improved slightly.
Aid agencies are concerned about hunger levels. The fighting has prevented farmers from planting crops in many parts of the state, and it is difficult to transport food or reach markets.
Insecurity and government restrictions put many of the displaced out of reach of aid, especially those in SPLM-N areas. People in these areas are particularly vulnerable to food emergencies, the Famine Early Warning Systems Network (FEWSNET) said.
In September 2011, fighting between SPLM-N and Khartoum forces in South Kordofan spread to Blue Nile state.
Sudanese President Omar Hassan al-Bashir immediately called a state of emergency in Blue Nile, sacked state governor Malik Agar of the SPLM-N, and closed SPLM-N's headquarters in Khartoum.
Sudan complained to the U.N. Security Council, accusing South Sudan of supplying rebels in both Blue Nile and South Kordofan with arms. Juba denies the charges.
Sudan has attacked villages with warplanes and troops, killing civilians and burning down settlements, refugees from the area have said. Sudanese army and civilian officials have denied the allegations, in turn accusing the rebels of using civilians as human shields.
As with South Kordofan, the government has restricted aid agencies' access to people in need in Blue Nile.
In August 2012, the United Nations helped broker a deal between Khartoum and the SPLM-North to allow food, via Sudanese soil, into rebel-held areas in both Blue Nile and South Kordofan states.
In March 2013, the government allowed aid agencies to visit all six areas in Blue Nile, for the first time since September 2011. They found tens of thousands of people in need of aid – both people who had been displaced, and residents.
But in May 2013, U.N. humanitarian aid chief Valerie Amos said the SPLM-N was stopping the United Nations from crossing from government-controlled areas into rebel-held areas, and insisting the UN cross via international borders – South Sudan or Ethiopia.
People living in SPLM-N controlled areas are particularly vulnerable to food shortages and famine. Many are unable to farm and have no access to humanitarian aid, depending instead on wild foods, FEWSNET said.
Tens of thousands have been displaced, and many have fled to South Sudan and Ethiopia. A few thousand have since returned from Ethiopia, and they need food, health care and shelter, FEWSNET said.
Blue Nile state is inhabited by an array of communities, deeply divided between “indigenous” people and Arab and non-Arab “newcomers”. The area has long been marginalised, its natural wealth mostly enriching elites in Khartoum who do not share power and redistribute resources, ICG says.
Under the 2005 peace deal, Khartoum was required to reduce its forces to prewar levels in Blue Nile. But governor Agar said more than 20,000 troops were still stationed there at the end of 2010 on the eve of South Sudan's referendum. The Small Arms Survey says there were also large, but unverifiable, numbers of Popular Defence Forces – a pro-Khartoum militia. Towards the end of 2010, SPLM forces moved into the area.
People in Blue Nile were not granted a referendum to choose whether to join north or South Sudan under the 2005 peace deal. Many who sided with the southern rebels in the civil war felt betrayed.
The peace deal did however call for popular consultations on the state's status, to be held in 2011. The process allowed 76,000 Blue Nile citizens to air their grievances, and the SPLM used this to push for self-rule.
The consultations were supposed to be finalised before South Sudan’s July 2011 independence but, once that deadline passed, Sudan’s ruling National Congress Party was even less inclined to share power or allow local autonomy, ICG says.
SPLM-N was supposed to become an opposition political party after July 2011, but it still had troops, which Khartoum wanted to expel or disarm rapidly. This led to the resumption of war in South Kordofan and Blue Nile.
A last-minute deal between the NCP and the SPLM-N, the 26 June 2011 framework agreement, brokered by the African Union and late Ethiopian Prime Minister Meles Zenawi, was rejected by President Bashir.