An Islamist rebel movement in Mali says it now controls the main towns in the country’s vast northern region after ousting the secessionist Tuareg fighters who first launched an uprising against the government earlier this year.

The declaration late on Thursday by Ansar Dine, which has links to al-Qaeda militants, will add to concerns that northern Mali could become a stronghold for jihadi groups and criminal gangs.

It follows clashes on Wednesday in the town of Gao between Ansar Dine fighters and the Tuareg separatists, known as the National Movement for the Liberation of Azawad (MNLA). At least 20 people were killed, and the MNLA was forced from the town.

Ansar Dine and its Islamist allies were already in control in Kidal and Timbuktu, the two other main towns in the desert north, and reports from Timbuktu said that MNLA fighters had abandoned their main base at the airport on Thursday.

“Our men control all three of the towns in northern Mali,” Oumar Ould Hamaha, a Timbuktu-based Ansar Dine official, told Reuters.

“They [the MNLA] all ran away, we decided not to pursue them . . . All I can tell you is that they are not even in the outskirts of the city [Gao].”

The MNLA confirmed its forces had retreated from Gao, but said its men would regroup to defeat “Islamist groups that are terrorising our population”.

The MNLA launched the rebellion against Mali’s government in January. It was the fourth uprising since independence in 1960 by Tuareg militants, who have long protested what they say is the marginalisation and underdevelopment of the region. They entered into a loose military alliance with Ansar Dine, a newly formed Islamist group, and together were able to defeat Mali’s demoralised army.

A military coup in the capital Bamako on March 22 saw the army retreat from the north, allowing the rebels to seize control.

The bond between the MNLA and Ansar Dine was never strong. The MNLA wants independence for northern Mali, or “Azawad”, as a secular state. Ansar Dine rejects partition, but seeks to install strict sharia law, which it has already imposed in northern towns, banning television and football and preventing women leaving their homes alone.

Neither group enjoys wide support among residents of northern Mali, where the Tuaregs are only one of several ethnic groups.

Ansar Dine’s greater military strength appears to be a result of its recruiting foreign fighters from elsewhere in the Sahel and as far afield as Pakistan, as well as its alliance with other well-trained jihadi groups. It also has better funding, thanks to its links with al-Qaeda in the Maghreb (AQIM), a terrorist organisation that has earned many millions of dollars through the kidnapping of western hostages.

AQIM leaders have been regularly seen in northern Mali in recent months. An Algerian television station, Ennahar TV, reported on Thursday that Mokhtar Belmokhtar, one of AQIM’s founders, had been killed in the clashes in Gao. This has not been confirmed independently.

Ansar Dine has also linked up with a new jihadist group, the Movement for Unity and Jihad in west Africa, which has fighters in Gao.

Though Mali’s coup leaders have technically handed over authority to a transitional government in Bamako, the political situation remains fragile, and the prospects of the army attempting to retake the north any time soon are slim.

West African heads of states have proposed sending in a regional force to help restore Mali’s territorial integrity, but the junta is opposed to any outside intervention.

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