The evening light throws pink feathers across the sky. A herd of goats sends dust spiralling into the air and as it settles, a sand-coloured twilight descends on the sand-coloured city. In front of the mud construction of the Sankore mosque, men lie chatting in the sand. It absorbs their voices. Timbuktu sinks murmuring into an early night.

Somewhat incongruously, we arrive by plane. Timbuktu, in the east of Mali, on the southernmost edge of the Sahara, the eternal European metaphor for the back of beyond, for the unreachable. Not far from here, the paths that head for another form of unreachable begin, the paths of migration to Europe, through the deadly reaches of the desert. It all depends on which part of the world you chose to construct your myths from: this is Timbuktu's story.

One thing it certainly is not is the end of the world. For centuries, Timbuktu was a centre of the southern hemisphere, a stronghold of trade, an Islamic university city. Where the Niger Delta met the desert, the paths of ages crossed: from the North came the caravans, over the river came gold from West Africa. And after the merchants came scholars; Timbuktu was a cosmopolitan city. Our men murmuring into the evening are lying in the exact spot where West Africa's Quartier Latin lay in the 15th century, or to be more precise, a Quartier Arabe with 25,000 students. Almost the population of Timbuktu today.

Deceptive, this sand-coloured silence, the sense of being lost to the world. With a stoic pride the inhabitants of Timbuktu register the recent flurry of interest in something that has always been theirs: the oldest library south of the Sahara. Its Arab manuscripts dating back to the 13th century have brought state presidents, scholars, representatives of major foundations traipsing awkwardly through Timbuktu's sand to see them. Over 100,000 manuscripts on Islamic law, philosophy, medicine, astronomy, on termite-eaten parchment, on gazelle hide even.

There is no room for all this erudition in today's image of Africa. Which is why, opposite the Sankore mosque, in the light of a single, precious floodlight, stands a fancy new research centre, beamed as if by magic into the sparse historical settings. Elegant, air-conditioned, mud hut meets modernism. A gift from South Africa, a gift from rich to poor Africa – so that the continent can look back on its history with pride.

Timbuktu as a site of African renaissance, where the continent can reflect on its culture and its strengths - this was Thabo Mbeki's idea, as president of South Africa. On a state visit to Timbuktu he visited the Ahmed Baba Instititute, where 30,000 manuscripts are stored under state supervision. The institute bears the name of Timbuktu's most famous philosopher, but what a meagre place, how ill-suited to the restoration of so precious a heritage! Mbeki pledged his support; it was crucial to "raise Africa's profile, not only in the eyes of the world, but in the eyes of Africans themselves." Back in South Africa, he mobilised private capital and within a fortnight, the first experts from the Cape had landed in Mali. The Malians were bowled over by this display of efficiency.

Mbeki was replaced long ago, entire football stadiums have been erected in South Africa since then, and in Mali, where everything happens at a slower pace, the new Ahmed Baba Institute is finally ready for occupancy. Beautiful and alien it stands in the centre of Timbuktu, in the exact spot where the philosopher Ahmed Baba once lived; the South Africans insisted on the location, forcing the Malians to knock down their Gendarmerie. Now they are concerned that the gift will consume more energy that everything else in Timbuktu combined. An African-African partnership, two different worlds.

Africa as a continent without history - this image was corrected by the German explorer and scholar Heinrich Barth, after he studied the African chronicles in Timbuktu in 1853/54. And yet, a hundred years later, still very little was known about the African written history. Priceless manuscripts, stolen by France during its colonial rule in Mali, lay unstudied in the National Library in Paris. The British Africanist John Hunwick began his manuscript research in 1965 - without any idea of the wealth of texts that would emerge.

The majority of these are privately owned; the families in Timbuktu are only gradually starting to open the old chests in which they have stored and hidden the yellowed and gilded calligraphies for generations. The media hype created a new myth: Timbuktu was having its last secret wrested from its hands, "desert scrolls" on which the hidden history of the continent was chronicled. Indeed it is the libraries more than anything that prove "that Africa has shared in Islamic knowledge for almost a thousand years", according to the German Islam scholar Albrecht Hofheinz, who is overseeing a project for the digitalisation of the manuscripts at Oslo University. Some of them stem from Andalusia, North Africa and the Middle East, others were written by African writers in Timbuktu. African languages were also transcibed in the Arabic script for diplomatic correspondence and contracts.

Arabic played a similar role in parts of Africa that Latin played in Medieval Europe, it was the written language of the elites for centuries. Until the arrival of the French. The imposition of the French language was "devastating" for the scholarly tradition of the region, John Hunwick noted. Young Africans today often have no idea that a tradition of reading and writing even existed prior to the colonial era. In South Africa the ministry of education ordered a reappraisal of school books and curricula. The conclusion was that Africa's place in the world was related from a "overwhelmingly Eurocentric" perspective. For Shamil Jeepi, a historian at Cape Town University, Timbuktu is exactly the right place to disempower once and for all "the European colonial project" of historical denial. The university is helping with the evaluation and preservation of the documents.

There are also plenty of Malians who know nothing of their cultural history. In a mud hut, far away from Timbuktu, the farmers glance at one another in embarrassment when asked about the manuscripts. Hurriedly they send for a boy who has spent the most years in school; he stares shamefaced at the floor.

It is easy to lock a poor country in a smothering embrace. Gaddafi declared Timbuktu his home, and lavished it with gifts. A vast construction site on the outskirts of the city: another centre for manuscripts. No one needs it, but the "Gaddafi Center" must be more impressive that the South African building. A race for influence over the continent, played out on a small stage of sand and parchment.

At the end of Ramadan, Libyans drove through the night to Timbuktu in trucks and threw food parcels in front of the inhabitants' houses. "The Libyans have no manners", the recipients of these gifts said quietly. Then came Gaddafi's appearance, on the birthday of the Prophet. He was invited to eat a mechoui with Mali's president, the traditional festive desert meal. A chicken is stuffed with an egg, then a sheep with the chicken - but Gaddafi never turned up. He left the other guests sitting there, with their mutton, chicken and egg, and roared off to Timbuktu, to glory in the crowds alone.

All this fuss has created a stubborn new confidence in the owners of the manuscripts. No one embodies this more than Abelkader Haidara, whose father left him a library containing 9000 manuscripts, which he tends with profound erudition and love. Once upon a time, the charming, rotund Haidara convinced family upon family to hand over their manuscripts to the state; now the 45-year old preaches the opposite. "Hold on to your intellectual property!" He was the first to open a family library to the public; now Timbuktu has 32 private libraries.

When Haidara first sought foreign financial support a decade and a half ago, no one was willing to believe his story about an African library. The turning point came in the form of a black American: Henry Louis Gates. The head of African American Studies at Harvard was electrified when he saw the manuscripts and brought the Ford Foundation on board as a financial partner. Haidara giggles: "It's strange to think that this Gates became famous for a completely different reason." He was the man who was arrested on his own doorstep for supposedly trying to break in, and ended up drinking an anti-racist beer with Obama.

Haidara is about to bring out a CD of exemplary translations of his ancient manuscripts: "On conflict management and good governance. The Westerners all come over here thinking they invented everything."

Timbuktu tells of relations, perspectives. This was the way things used to be, when globalisation still rode on a camel's back. And this is how it is today, when Facebook users call themselves "Tim Buktu" with no idea that blogs and Facebook have been there for years. In the three-way relationship between Africa, the West and Islam, how do the sides perceive one another?

Since its founding in the 12th century, Timbuktu was Islamic. As an academic centre, the city came to embody the Islamisation of Africa - and the Africanisation of Islam. Every second African today is Muslim – a fact which is often overlooked. There is an inscription in Mali's National Museum which contains these remarkable words on the subject: With the creation of an indigenous class of Muslim scholars "Islam ceased to be the religion of a white foreigner and became an African religion."

The Arab "as white foreigner" – this does not refer only to the arrival of Islam. No one in Timbuktu has forgotten how the Moroccans conquered the city, plundered the libraries and dragged off the best scholars to Fes. Ahmed Baba, the philosopher, in chains! This is a source of embarrassment in Morocco today but the stolen manuscripts have yet to be returned to Timbuktu.

"We were also colonised by the Arabs," says Mohamed Dicko, director of the Ahmed Baba Institute. "It was an intellectual, cultural colonisation and it is still at work today in the notion that everything good about Islam came from the Arabs. It is like during the French colonial era when school children were taught only French writers." Soon, for the first time, texts in Arabic by native Mali authors will be appearing in textbooks, he says. His institute also receives money from Saudi Arabia, but Dicko plays that down, he prefers the South African partners. Amazingly the guardian of the manuscripts talks no Arabic: rumour has it that this was a deliberate political decision.

Is is possible to strengthen the Arabic heritage without allowing more Arab influence in the country? Saudi Wahabists have been trying for a long time to establish a "cleansed" de-Africanised Islam in Mali. They have had no success in Timbuktu so far; even the religious students still wear fetishes.

If you talk to Abdramane Ben Essayouti, Timbuktu's leading imam, about the Wahabists, he straightens his bright blue robe, the bubu, and relates a famous anecdote: When in 1324 the Malian King Kankou Musa went on a pilgrimage to Mecca, his caravan was loaded with so much gold that while he was on the road, the value of gold in Cairo plummeted. "Saudi Arabia," says the Imam with a subtle smile, "was just a sandpit in those days". When the King returned he brought an architect with him who set to work building Timbuktu's cultural heritage for the future. The Djingareyber mosque is still standing 700 years later and Ben Essayouti is its imam. "The Wahabists will not be able to do anything about a tradition as strong as ours."

Ben Essayouti owns 8,000 ancient manuscripts and an internet cafe. The 14th century is in the vitrines, the 21st in is the basement – no distance at all for the man in the blue bubu. "I was the first to get an email address": imamtombouctou. He took his children out of the French-speaking state school and sent them to an Arabic-French lyceum, a day's travel away. So that one day they will be able to accept their inheritance appropriately informed. Recently a European tourist offered him a handsome sum for a manuscript of astronomical calculations.

The Imam smiles subtly. Of course it was not for sale.

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This article was originally published in Die Zeit on March 25, 2010.

Charlotte Wiedemann is a freelance journalist who specialises in reportage from Africa and the Middle East.

Translation: lp