The seizure of Timbuktu by a fractious group of separatist and Islamist rebels in northern Mali has raised fears for the fate of the legendary city's ancient manuscripts and architectural treasures.

Timbuktu, a cradle of Islamic learning and a thriving trade centre in its 16th-century heyday, was overrun Sunday by Tuareg separatists and Islamist rebels.

Witnesses said the Islamists then chased the Tuareg fighters from the city, increasing fears the accelerating violence since Mali's government was overthrown in a coup could endanger Timbuktu's rich archives and historic mosques.

"Unique manuscripts have been conserved for centuries in Timbuktu, a scholarly city, a city of 333 saints, where practically every household is a heritage site, a library," Hamady Bocoum, head of African research institute IFAN, told AFP.

"I think there are serious risks to those manuscripts."

Mali has been in turmoil since a band of low-ranking army officers ousted the government on March 22, saying President Amadou Toumani Toure had failed to stand up to the Tuareg insurgency.

The power vacuum played into the hands of the insurgents, who have captured key towns in the vast arid north virtually unopposed.

The fall of Timbuktu, followed by in-fighting between the motley crew of Tuareg and Islamist rebel groups, has kept the city and its history under threat.

Timbuktu is home to nearly 100,000 ancient manuscripts, some dating to the 12th century, preserved in family homes and private libraries under the care of religious scholars.

At its height in the 1500s, the city, a Niger River port at the edge of the Sahara, was the key intersection for salt traders traveling from the north and gold traders from the south.

It was also a renowned centre of Islamic scholarship, with manuscripts written in Arabic and Fulani by scholars of the ancient Mali empire, covering a range of subjects including Islam, history, astronomy, music, botany, genealogy and anatomy.

Bocoum worried manuscripts could be illegally sold or destroyed by the "new arrivals", who reportedly include Al-Qaeda in the Islamic Maghreb, the north African branch of Al-Qaeda.

"These manuscripts have survived through the ages thanks to a secular order, in an area of trade where all the region's peoples intersect. With the arrival of the Islamists, that secular order is broken, that culture is in danger," he said.

The United Nations cultural agency UNESCO also issued a plea Tuesday to protect the city's history.

"Timbuktu's outstanding earthen architectural wonders that are the great mosques of Djingareyber, Sankore and Sidi Yahia must be safeguarded," said UNESCO director-general Irina Bokova in a statement.

She called the city "essential to the preservation of the identity of the people of Mali and of our universal heritage".

UNESCO added Timbuktu to its World Heritage List in 1988 in recognition of its status as a legendary trade hub and its history stretching back to the 5th century.

The owner of one of the city's private libraries said he fears for his collection.

"I really don't know at the moment what's going to become of my manuscripts," he said.

"I'm waiting. But frankly I'm afraid."