Arriving in Timbuktu after a long, hot journey across the Sahara, you come to a striking monument to peace, with guns embedded in concrete. It was built in 1995 to commemorate the ceremonial burning of 3,000 weapons at the end of the last Tuareg rebellion.

Today, the black flag of Islamist rebels flies over this fabled city and it is once more at the centre of conflict. There are reports that 300 Christians, whose families have lived there for centuries, have fled the city amid the imposition of rigid sharia law. Women have been told to cover up, Western dress banned and looters threatened with beheading.

Yesterday's declaration of independence in the north of Mali marks the culmination of a depressing fortnight that has ripped apart this beautiful nation, for two decades such a model democracy.

It all began on 21 March, when a barracks mutiny turned into an accidental coup. Soldiers, infuriated by lack of supplies and political support to crush a two-month rebellion in the huge northern desert region, ended up in control of the capital under an army captain who is out of his depth.

Given the troops' complaints, there is savage irony to the speed with which the rebels exploited the chaos to sweep through key Saharan towns. The question, however, is precisely who is in control? The most prominent rebel group is the MNLA, who take a relaxed approach to religion. Tuareg women tend to go uncovered while men drink, smoke and dance – exemplified by the famous Festival in the Desert.

But there are fears they are being sidelined by Ansar Dine, a smaller Islamist group that returned well-armed and battle-hardened from the fighting in Libya. Lurking in the background is al-Qa'ida in the Islamic Maghreb, an autonomous terror group behind a spate of kidnaps and killings.

It all adds up to a bleak outlook for Mali, with aid stopped, sanctions imposed, a political void in the south and rising threat of a full-blown civil war, theocracy and a refugee crisis in the north. This is not just a nation with a glorious heritage, but the strategic hub of a highly volatile region. The world needs to wake up to what is happening.

twitter: @ianbirrell