MALAKAL, Sudan — Thousands lined up in South Sudan Monday to divide Africa's largest country.

The South Sudanese were registering to vote in the Jan. 9 referendum for independence from northern Sudan. There is no doubt here that the vote — if free and fair — will be to split Sudan in two.

But the vote for independence has dangers and tensions are rising. There are fears that the poll could spark a return to the north-south conflict that raged in Sudan for much of the last 50 years.

U.S. President Barack Obama hailed the opening of the voter registration as a "critical milestone." Hollywood star George Clooney has said that the vote for independence of the south is crucial for peace and stability.

The Comprehensive Peace Agreement (CPA) brokered by the United States and others in 2005 ended the most recent round of fighting, which lasted 22 years and led to the deaths of an estimated 2 million people.

In the town of Malakal on the banks of the Nile River the sun was still low in the sky as ethnic southerners — the vast majority in this mixed trading town — lined up to register.

“I want separation,” said Kahn Nit, a 35-year old education expert working for an international organization. “We suffered for a long time but it is better to push the Arabs out by voting rather than by shooting guns.”

The decades-long, north-south war pitted Arab Muslim northerners against mostly Christian southerners in a battle over religion, ethnicity and oil.

The peace agreement laid out a roadmap that included national elections held in April this year and the referendum due in January, in which ethnic southerners — in the north, south or abroad — will choose between unity and secession. The registration period will last for 17 days to allow an estimated 5 million potential voters to be listed at around 3,000 centers.

“It is a very important moment now, we have been waiting so long for this,” said Simon Kun Puoch, governor of Upper Nile State, brandishing his new thumb-printed and laminated voter card.

“This card determines my future. It is my most precious possession now, if I don’t have it then who am I?” he said.

Who has, or does not have, voter cards is a worrying issue for many southerners who have over the years of fighting lost all trust in the northern government based in Khartoum and run since 1989 by President Omar Al Bashir. Two years before the peace agreement was signed another war erupted in the western region of Darfur, again over oil, ethnicity and religion.

Employing tactics battle-tested during the north-south civil war, Bashir ordered aerial bombardments and unleashed militias that attacked civilians and combatants alike. For ordering those attacks Bashir was charged with war crimes, crimes against humanity and genocide by the International Criminal Court in The Hague.

With between 500,000 and 1.5 million southerners living in northern Sudan there are fears that Khartoum may seek to inflate the number of registered voters in the north and then force people to vote for unity or block them from voting altogether in the hope that turnout falls below the 60 percent threshold for it to be valid.

“What will help Sudan to be secure will be allowing the south to decide for itself whether it wants unity or separation,” said Daniel Leau Luak, a retired teacher in his 70s who sat sharing cups of milky coffee with a friend in the market in the heart of Malakal.

“But this is also what will bring conflict because the north will try to force unity at all costs,” he said.

The African Union is leading efforts to mediate some of the sticky issues over border demarcation, oil and a region called Abyei that is supposed to hold a separate referendum on self-determination at the same time. At the weekend it said that a “soft border” had been agreed between the northern National Congress Party (NCP) and the southern Sudan People’s Liberation Movement (SPLM).

Both sides agreed to allow nomads to cross over and trade to continue which might help defuse growing tensions, especially in the frontier region where northern and southern troops are being redeployed to an unclear and disputed border line. Earlier this year Secretary of State Hillary Clinton called Sudan “a ticking time bomb” and she is not alone in fearing a resumption of fighting.

“Every southern Sudanese wherever we are we want our freedom, freedom from the north which has fought us and committed injustices over all these years,” said Suzanne Jambo, a senior SPLM official.

It is hard to argue with Jambo’s assertion that southerners will, in a free and fair referendum, vote overwhelmingly for independence and she issued a warning: “Expectations now are so high, tempers are so hot that any interference [from the north] could lead to … anything," she said. "If you

want to force me into unity with the north I will go to war.”