JUBA, Sudan—The polls are closed and the ballots have been cast. By mid-February, the world will learn whether Southern Sudanese voters voted to create a new, independent state -- as initial results suggest that they overwhelmingly did. But as rapturous as independence will be for the south, there's good reason to fear that secession will leave the governments of both Sudans reeling. In Khartoum, President Omar al Bashir faces mounting political opposition -- and for the first time in years, he looks weak, as he braces for the imminent loss of the most oil-rich region of his state. In Juba, a new country must be built from the ground up. And the risk that the new Southern Sudanese state could follow the examples of its regional peers -- from Ethiopia to Uganda -- and disown democracy somewhere down the road is very real. What is today one troubled Sudan may soon become two fragile states struggling to stay intact, with leaders struggling to stay in control.

The south's weeklong independence referendum, which ended on Jan. 15, was completed without violence or other any significant disruptions. A few days into the counting process, most of the international observer missions watching the vote had already issued statements  declaring it to have been credible and up to international standards. The referendum commission's preliminary results, posted online, show most areas of the south at more than 99 percent in favor of secession.

Since 2005, when a peace agreement was signed to end decades of civil war with the north, Juba has operated autonomously -- and gotten off to a surprisingly promising start. But after independence, Juba will have to start building its own institutions and delivering visible results to an eager population that has been waiting decades to be free. Expectations are high, even as the challenges remain dire. The new country will boast a youthful and unemployed population, an utter lack of development, and a bloated and internally divided army. Infrastructure will have to be built from scratch, extending into the far reaches of the territory where "remote" takes on a new meaning: Vast swathes of the southern territory are accessible only on foot or in a U.N. helicopter.

The elected officials who must tackle these challenges have little experience in government. Many of the ministers currently serving in Juba were instrumental in the south's struggle for independence, having been commanders in the rebel army or leaders of the political wing of the movement. Few have ever worked in civilian jobs. Nor can they count on a wealth of talent below them; in the ministries of finance, agriculture, and education, there are only a handful of trained and literate civil servants. Government payrolls are clogged with ghost workers -- supposed employees who continue to receive salaries but who no longer work there or are dead. As ministries sort out the fake names from the actual employees, real teachers are going unpaid and clinics are without the usual government-donated medicine. Then there is the perennial issue of patronage. Many ministerial offices in Juba now prominently display signs designating certain times as "personal" visiting hours, in an attempt to keep people from lounging in offices all day as they wait to submit their request for personal funds to their-uncle-the-minister.

But perhaps the greatest challenge for an independent southern government will be to overcome the growing internal threats to its authority without resorting to repression. Inter-communal conflict in the region is common -- and seemed to be escalating in 2010 as competition for scarce resources grew. Rival ethnic groups will likely be watching how their interests are represented in a new government. In managing those potential conflicts, Juba will need to avoid the lessons of its northern neighbor. Through his two decades of rule, Bashir has used the state's military apparatus to suppress insurgencies, often enlisting local proxy militias and external arms suppliers to help. Southern Sudan's people and its leaders have lived in such a state for much of their lives.

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