"We are worried about our future after secession because Somalis are considered pro-Northern Sudan because we are all Muslims," Ahmed Mohamed, a Somali businessman in Juba, capital of Southern Sudan, told IRIN.
"I am from Somaliland [a self-declared independent republic in Somalia], which has a lot of similarities with the Southern Sudan, but we are Muslims. Southern Sudanese people have sensitive thoughts about Islam, because they consider it a tool used for their oppression by the Northern Sudan government in the last decades."
Ibrahim Abdalla Sheikh, an imam at a mosque in Juba, said he hoped Muslims were not in any danger.
"More than 30 percent of the Bari community in Southern Sudan are Muslim and we hope nothing will happen to us whether or not the South becomes an independent state," he said. "Of course Islam is the largest religion in [Northern] Sudan, but in the South we are the minority."
It is expected that the Southern population will vote overwhelmingly for secession in the referendum that began on 9 January.
There are an estimated 5,000 Somalis living and working in Southern Sudan. Many have businesses, mostly dealing in food and fuel.
Mohamed Ali, a Somali shopkeeper in Juba, said: "We are worried that if Southern Sudan separates from the rest of Sudan, the Southerners may say, 'Somalis have taken our businesses', as has happened in South Africa."
However, Dr Barnaba Marial Benjamin, Minister of Information for Southern Sudan, assured the Somalis and other Africans in the region they would be safe.
"Somalis and other Africans who have businesses here will have nothing to worry about whether we get our independence or not," he said.
Somalis fleeing the civil war at home have established businesses in many parts of Africa, particularly in Kenya. Many Somalis have suffered xenophobic attacks in South Africa.
''We are worried about our future after secession because Somalis are considered pro-Northern Sudan because we are all Muslims''
Somalis are freaking everywhere.... thought all the Somalis in Sudan lived in Khartoum/Omdurman