See a Magnum Photos gallery on South Sudan.
Other Arabs, traders who've lived here in Malakal and other cities for decades, have fled north, as well. Some will stay put. Others are waiting to see if the south remains at peace before returning with their stock.
A far bigger migration is taking place from north to south. More than 120,000 southerners have abandoned their homes in Khartoum and other cities to throw in their lot with the new state. One night last week, at an open-air way-station in Omdurman, just across the Blue Nile from Khartoum, groups of southern men and boys stood watch over piles of bed frames, mattresses, and peeling bureaus, waiting for the trucks and buses that would take them south.
It was southern nationalism—pure and simple—they said, that had motivated them to leave at this time, after decades of relative security in the north. Alone, away from the group, one man admitted that he and many of his friends had been shaken by a speech last month in which President Bashir promised a resurgence of sharia law. (The future, Bashir said, would be "no time to speak of diversity of culture and ethnicity," an odd contention given that even without the south's 8 million blacks, Arabs will still not form a majority in the new, truncated Sudan.)
The migrant influx has proved to be more than the south can handle. At least 22,000 people arrived recently to one dusty pocket of Northern Bahr El Ghazal state, where they joined 5,000 others displaced last year from their homes near the border by northern bombers. After days on the road with little food and water, many newcomers are sick and weak.
"While the entire world focuses on the referendum on self-determination, we are seeing an existing humanitarian emergency grow rapidly worse and overwhelm the local capacity," Susan Purdin, who oversees the International Rescue Committee's programs in southern Sudan, said in a statement.
The biggest tension has not been in the south at all, but in the hotly disputed region of Abyei, which is torn between the southern Ngok Dinka tribe and Arab Misseriya nomads, who use Abyei as a traditional watering ground for their herds. Similar disputes occur elsewhere along the still-undemarcated border between north and south, but Abyei sits on top of oil, making it a more worthy prize.
Sudan's Comprehensive Peace Agreement called for a referendum to be held this week, in which residents of Abyei would decide whether they wished the region to remain in the north or to become part of the south, but that vote has been postponed after disagreements over who would have the right to participate. At least 30 people have been killed in Abyei in clashes that began on Friday.
For once, tension and fear of gunfire seem far away from Malakal. This Nile port city saw two major battles between northern and southern forces, in 2006 and again in 2009, that left more than 400 people dead (not to mention a 2007 skirmish that found me hiding in a brick-walled outhouse), but that seems like another era.
At 3 a.m. on Sunday, 40-year-old Natal Onane Charles woke up in his mud and reed house, slipped on a gray suit, a fraying white Oxford shirt, green socks, and brown boots, and set out alone in the cold for the primary school that would serve as his local polling place. He said he felt skittish at first, walking alone in the mist, but he pressed on until he reached the town.
"When I got to the polling station, my friends were already standing in line, them and 50 others," he said. "They told me, 'Where have you been? You are late.' "