TIMBUKTU, Mali — When the moment of danger came, Ali Imam Ben Essayouti knew just what to do. The delicate, unbound parchment manuscripts in the 14th-century mosque he leads had already survived hundreds of years in the storied city of Timbuktu. He was not about to allow its latest invaders, Tuareg nationalist rebels and Islamic extremists from across the region, to destroy them now.
So he gingerly bundled the 8,000 volumes in sackcloth, carefully stacked them in crates, then quietly moved them to a bunker in an undisclosed location.
“These manuscripts, they are not just for us in Timbuktu,” Mr. Essayouti said. “They belong to all of humanity. It is our duty to save them.”
The residents of Timbuktu suffered grievously under Islamic militant rule. Almost all of life’s pleasures, even the seemingly innocent ones like listening to music and dancing, were forbidden. With the arrival of French and Malian troops here on Jan. 28, life is slowly returning to normal.
But the city’s rich historical patrimony suffered terrible losses. Timbuktu is known as the City of 333 Saints, a reference to the Sufi preachers and scholars who are venerated by Muslims here. The Islamic rebels destroyed several earthen tombs of those saints, claiming such shrines were forbidden.
During their hasty departure from the city last weekend, the fighters struck another parting blow, setting fire to dozens of ancient manuscripts at the Ahmed Baba Institute, the city’s biggest and most important library.
Irina Bokova, the director general of Unesco, accompanied President François Hollande of France on his visit here on Saturday to get a firsthand look at the damage the city’s cultural artifacts had sustained. She said that plans are already being made to rebuild the tombs of the saints.
“We are going to reconstruct the mausoleums as soon as possible,” Ms. Bokova said. “We have the plans, we have the ability to do it. We think this is important for the future of the Malian people, their dignity and their pride.”
In modern times Timbuktu has become a synonym for a remote place. But the city thrived for centuries at the crossroads of the region’s two great highways: the caravan route across the Sahara passed right by its narrow warren of streets, bringing salt, spices and cloth from the north, and the Niger River brought gold and slaves from West Africa. Traders brought books, and the city’s scribes earned their living by copying them out by hand. These manuscripts cover a vast range of human knowledge — Islamic philosophy and law, of course, but medicine, botany and astronomy as well.
“You will find all forms of knowledge in these manuscripts,” Mr. Essayouti said. “Every topic under the sun.”
Beyond their physical presence, Timbuktu’s artifacts are a priceless reminder that sub-Saharan Africa has a long history of deep intellectual endeavor, and that some of that history is written down, not just transmitted orally down the generations.
“This is the record of the golden ages of the Malian empire,” Ms. Bokova said. “If you let this disappear, it would be a crime against all of humanity.”
The cultural artifacts in Timbuktu — whose population of around 50,000 has shrunk with the latest troubles — have faced many dangers over the centuries. Harsh climate, termites and the ravages of time have taken a toll, along with repeated invasions — by the Songhai emperors, nomadic bandits, Moroccan princes and France. Yet many of the antiquities have endured.
“It is a miracle that these things have survived so long,” Mr. Essayouti said.
Their survival is a testament to the habit of Timbuktu’s families of hiding away their valuable relics whenever danger is near, burying them deep in the desert.
Konaté Alpha’s family has had a collection of about 3,000 manuscripts for generations, and when the Islamist rebels arrived Mr. Alpha called a family meeting.
“We need to find a way to safeguard these manuscripts,” he told his brothers and his father.
He was intimately familiar with the many nooks and crannies in which the city’s residents have long hid their treasured manuscripts. While expanding the family’s compound a decade ago, he found a trove of manuscripts hidden inside a wall.
“The previous owners had hidden them so well they forgot them,” he said with a shrug.
He took his family’s collection and hid it well. He declined to say where.
“We hid them, that is all I will say,” he said.
The manuscripts have been at the center of a broad international effort to preserve the fragile history of Timbuktu. The governments of South Africa and France, along with the Ford Foundation and others, have spent millions to build a new library to house the largest and most important collection of manuscripts at the Ahmed Baba Institute.
When the Tuareg rebels first arrived in Timbuktu in April, they looted and burned many government buildings, and the institute’s interim director, Abdoulaye Cissé, worried that the institute’s sleek new library building would become a target.
But when the Islamist rebels arrived a few days later, the library’s officials explained to them that the library was an Islamic institution worthy of their protection.
“One of the Islamist leaders gave his mobile phone number to the guard and told him, ‘If anyone bothers you, call me and I will be here,’ ” he said.
But library officials began to worry that the Islamists would discover that the library received financing from the United States, so in August they decided to move almost the entire collection, Mr. Cissé said.
“We moved them little by little to avoid rousing suspicion,” Mr. Cissé said. They were sent to Mopti, then on to Bamako, the capital, for safekeeping.
It turned out the worries were not unwarranted. In the chaotic final days of the Islamist occupation, all that changed. A group of militants stormed the library as they were fleeing and set fire to whatever they could find.
Fortunately, they got their hands on only a tiny portion of the library’s collection.
“They managed to find less than 5 percent,” he said. “Thank God they were not able to find anything else.”
None of the city’s libraries are in a hurry to return their collections from their hiding places, even though Timbuktu is back under government control. French forces are now stationed in Gao, Timbuktu and outside the town of Kidal, in the north, and airstrikes continue against the militants near the border with Algeria. The fighters have been chased away from major towns, but no one is sure whether they will come back.
“We will keep our manuscripts safely hidden until we are sure the situation is safe,” Mr. Alpha said. “When that will be we cannot say.”