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KHARTOUM (Reuters) - Sudan's military has killed the leader of Darfur's most powerful rebel group, dealing a severe blow to insurgents in the remote western region and complicating a nearly decade-long war with Khartoum in which hundreds of thousands are believed to have died.
The Darfur conflict has rumbled on since mainly non-Arab insurgents took up arms in 2003, saying the central government had left them out of the political and economic power structure and was favouring local Arab tribes.
Khalil Ibrahim, head of the Justice and Equality Movement, emerged as one of the most powerful rebel commanders. In 2008, his fighters drove across the arid western terrain and launched a shock attack on Khartoum, killing over 200 people.
Sudan's authorities have long hunted Ibrahim, who had taken refuge in neighbouring Libya under Muammar Gaddafi until the leader's overthrow deprived him of his safe haven, and had refused to sign a Qatar-brokered peace deal.
Al-Sawarmi Khalid, Sudan's armed forces spokesman, said government troops killed Ibrahim as he tried to cross into South Sudan, which seceded in July under a 2005 peace deal that ended a separate, decades-long civil war.
"The armed forces clashed in a direct confrontation with Khalil Ibrahim's rebel forces, and were able to eliminate Khalil Ibrahim, who died with a group of commanders," Khalid told state television.
JEM contradicted the military's account of its leader's death, however, saying Ibrahim died on Friday morning in an airstrike which also killed one of his guards. It said the precision of the strike suggested "collusion and conspiracy of some regional and international parties".
"The blood of the martyr will not go in vain, and those who assassinated him will pay the price many times over," the group said in a statement.
The death of Ibrahim, often described as a commanding and charismatic leader, could be a major blow to JEM, although restricted access to Sudan's conflict zones has made it hard to gauge the actual strength and internal unity of insurgents.
"Khalil Ibrahim dominated JEM and personally determined the movement's political and military strategy and in particular was responsible for JEM's posture of refusing negotiation with the Government of Sudan. His death is a very serious blow to the movement," Alex de Waal, a leading Sudan expert, said.
"The leadership in Khartoum will be tempted to respond to his death by considering that the insurgency in Darfur is now finished. While the threat posed by JEM is undoubtedly diminished, it would be an error for it to conclude that the political conflict in Darfur can be so readily resolved."
The United Nations has said as many as 300,000 people may have died in Darfur, where Khartoum mobilised troops and mostly Arab militias to crush the uprising. Khartoum puts the death toll at 10,000.
While violence has died down since the mass killings reported in the early days of the conflict, law and order have collapsed and the area has been hit by attacks by bandits, militias, soldiers and tribal groups in recent years.
Some 2 million people have fled the fighting, the United Nations says. The International Criminal Court has charged Sudan's President Omar al-Bashir with masterminding genocide and other crimes in the region, accusations Khartoum dismisses as political.
Various Darfur rebel groups, including two factions of the Sudan Liberation Army, have fought on despite a huge United Nations-African Union peacekeeping operation set up in 2007.
Qatar brokered a peace deal which Sudan signed this year with the Liberation and Justice Movement, an umbrella association of smaller groups.
But JEM and the other major rebel groups have refused to sign the document, dampening hopes the region will soon see lasting peace.
In November, Darfur's main insurgent groups said they had formed an alliance to topple Bashir with other rebels in two border states, where fighting broke out around the time of South Sudan's independence.
Islamist in its outlook, Ibrahim's group has cooperated in the past with the more secular SLA rebels, although their different ideologies and histories have led to tensions.
JEM has claimed military advances as recently as last week, saying on Saturday its fighters clashed with government militias in parts of the North Kordofan state and were planning to advance on the capital Khartoum.
"I don't think JEM will disappear with Khalil's death, but there's a risk that JEM fractures without his leadership, as has happened with the SLM and other rebel movements in Darfur," Aly Verjee, a researcher at the Rift Valley Institute think tank , said.
"In the short term, Khartoum's Darfur policy won't change - the agreement with LJM will continue, new state administrations will be appointed, and military action against JEM and its allies will continue."
Writing by Alexander Dziadosz; Editing by Michael Roddy