(Originally published in the Atlantic.com on June 22, 2011)

On July 9, southern Sudan will declare its independence from Sudan in accordance with the terms of the 2005 Comprehensive Peace Agreement (CPA) that ended the Second Sudanese Civil War, which lasted from 1983 to 2005. But with less than three weeks remaining before southern Sudan becomes the independent Republic of South Sudan, a growing problem threatens to complicate the process, and suggests that Sudan’s split may not go as peacefully as the international community had hoped. In the border state of South Kordofan, the rapid deterioration of the security situation and the region’s uncertain future could portend struggles ahead for Sudan’s two state future.

An ethnically and religiously diverse state, South Kordofan straddles Sudan’s North-South divide and includes the disputed sub-region of Abyei. South Kordofan is important not only for its oil deposits, but also for its fertile land, on which Nuba farmers and nomadic pastoralist Arab tribes depend for their livelihoods. Aside from its economic importance, the region has historically been central to the stability of Sudan, and is likely to remain so even when southern Sudan becomes a sovereign nation.

During the civil war, both sides sought control of the centrally located region. The regime in Khartoum, the capital, used it as a means to project control over the south, and the Southern People’s Liberation Army (SPLA) used it to extend the civil war to the north. Like southern Sudan, South Kordofan was one of Sudan’s marginalized peripheries. Southern Sudanese political and rebel leader John Garang, who died in a 2005 helicopter crash, advocated a concept of a united, secular, and democratic “New Sudan,” which resonated with the Nuba people of South Kordofan — many of whom joined the SPLA. The Nuba Mountains of South Kordofan rapidly became one of the frontlines of the civil war, witnessing some of the heaviest fighting. As part of its counterinsurgency strategy, Khartoum bombed the civilian population of this region indiscriminately; impeded humanitarian aid organizations from accessing populations in need; armed Arab tribal militias as proxies; targeted the land, livestock, water, and property of the local population to destroy their livelihoods; and forcibly relocated civilians into “peace camps” in order to separate them from the SPLA.

South Kordofan’s current instability can be traced in part to the failure of CPA implementation in this region. As stipulated in the CPA’s Protocol on the Resolution of Conflict in Southern Kordofan/Nuba Mountains and Blue Nile State, “popular consultations” were to be held through the elected state legislature so that the citizens of the state could address, and hopefully even resolve, any shortcomings in the agreement. As of yet, these have not taken place, due in part to the delays of the legislative and gubernatorial elections, which were held only last month. Consequently, many Nuba say they feel that the CPA was never fully implemented in South Kordofan, and that there is still no mechanism to address past injustices and local grievances. Perhaps most problematically, unlike southern Sudan, the CPA did not provide South Kordofan with the right of self-determination, which has left some Nuba feeling abandoned by its wartime allies. South Kordofan’s very serious problems — historical marginalization within Sudan and the ethnic tensions that have resulted from the civil war — are still not fully addressed.

In recent weeks, security in South Kordofan has deteriorated markedly. In mid-May, the internationally indicted war criminal and Khartoum-allied politician Ahmed Haroun defeated Southern People’s Liberation Movement (SPLM) candidate Abdel Aziz Adam al-Hilu in the state’s gubernatorial elections. The SPLM alleged that the elections had been rigged and refused to accept the results. On May 19, a Sudanese army convoy north of Abyei was attacked. Two days later, the Sudanese Armed Forces seized Abyei in response. The Sudanese Armed Forces and southern-aligned armed groups have skirmished since early June. The growing violence has so far displaced tens of thousands of civilians in South Kordofan and has detracted attention from crucial eleventh-hour negotiations on post-independence issues, such as the future allocation of revenues from Sudan’s oilfields, which likewise sit astride the North-South border.

As a very fragile southern Sudan prepares for independence, there is ample opportunity for the resumption of conflict in South Kordofan to destabilize the incipient nations — especially considering that southern Sudan is already being threatened by armed revolts based in the neighboring Unity and Upper Nile states. If there is to be a sustained peace between Sudan and the Republic of South Sudan, the CPA as it stands will not be enough. South Kordofan still carries the politicized and militarized baggage of the civil war. The region and its unresolved problems will risk perpetuating low-intensity conflict along the North-South border. If Sudan is to be peaceful, so to must South Kordofan, finally, reach its own peace.