The buried Bronze Age city of Mari on the Euphrates River in eastern Syria has been giving up its secrets to French and Syrian archaeologists since its discovery in 1933. But the Syrian civil war threatens the precious artifacts therein.

Forty-two excavation campaigns over almost 80 years have unearthed a 300-room palace, brilliantly coloured frescoes and more than 25,000 clay tablets written in cuneiform script, one of the earliest writing systems.

When fighting between the Syrian army and rebels brought work to an abrupt end in 2011 less than half the 60-hectare site had been uncovered. An unknown number of cultural layers lie below ground. Now an armed gang of treasure hunters equipped with bulldozers has supplanted archaeologists’ painstaking efforts with trowels, brushes and soil sifters.

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Mari is one of hundreds of Syrian historical sites under assault from international gangs of thieves “organised like the Mafia”, said Minister for Culture Dr Loubana Moushaweh when I interviewed her in Damascus recently.

Interpol has issued an alert for stolen Syrian antiquities and helped recover Roman mosaics trafficked into Turkey. More promisingly, the national museum network is largely secure, with almost all holdings documented electronically, Moushaweh says. This contrasts with neighbouring Iraq’s museums, which were left unprotected to suffer widespread looting following the US invasion in 2003.

Some of Syria’s six World Heritage historical areas have suffered serious war damage, but Moushaweh suspects the greatest losses will turn out to be the destruction of historical evidence and hitherto undiscovered riches as thieves dig for gold, jewelry, statues and mosaics at unguarded archaeological sites. Most of Syria’s archaeologically rich regions are in rebel hands.

A few kilometres from Mari is the walled Hellenistic and Roman city of Europos-Dura. The Syrian government submitted both of these Euphrates Valley sites for World Heritage listing in 2011, but they soon fell under the control of feuding rebel bands.

At Europos-Dura — explored by French, American and Syrian archaeologists since the 1920s — about 300 gang members are using heavy machinery to carry out “fierce excavation” that has destroyed 80% of the 56-hectare site with holes up to three metres deep, according to a recent report by Syria’s general director of antiquities and museums, Professor Maamoun Abdulkarim. Illegal digging sped up in September last year after someone found a gold bracelet at the site.

But Moushaweh, a former Damascus University dean appointed to head the ministry in 2012, says Mari is the site of greatest concern because use of earth-moving equipment had caused “irreparable damage”. Mari is thought to have been inhabited since the fifth millennium BC. Moushaweh says the gang has settled into the archaeological mission residence and visitor centre and is working off satellite pictures and using metal detectors.

“Theft of objects is not the main danger to archaeological sites,” she said. “It is the damage they are causing during excavation. I meet the head of the museum service on a daily basis, and we tally the damage nationwide.”

Aerial photographs show hundreds of ancient cities and graveyards “as cratered as the surface of the moon” following illegal digging, reported Erin Thompson, a US expert on art crime.

Syria’s museum network includes 21 internationally recognised artifact museums, and Moushaweh says her ministry has transferred valuable items out of all but one of them to secure locations. The one exception is the museum at Raqqa, the only provincial capital wrested from government control. Raqqa is currently run by the al-Qaeda affiliate ISIS (Islamic State of Iraq and the Levant), which has been busy destroying churches and staging public Bible burnings. Moushaweh says boxes of artifacts have been stolen from Raqqa museum, “but we still don’t know our losses there”.

“UNESCO has called for a co-ordinated international response to protect Syria’s ‘irreplaceable heritage’.”

UNESCO has called for a co-ordinated international response to protect Syria’s “irreplaceable heritage”. Among the worst affected World Heritage properties are the mediaeval core of Aleppo, including its 1000-year-old souk (bombardment, street fighting and arson), and the Byzantine Dead Cities south of Aleppo (excavation and looting).

The World Monuments Fund has put two mediaeval castles damaged by fighting — Qalaat al Mudique citadel and the imposing Crusader fortress of Krak des Chevaliers — on its watch list.

The International Council of Museums has published an “emergency red list” of Syrian cultural objects at risk to help international authorities identify the categories of items particularly vulnerable to trafficking. The list contains objects covering the most important periods of Syrian prehistory and ancient history, the Islamic era and Middle Ages as well as the Ottoman period.

UNESCO director-general Irina Bokova said protecting Syria’s heritage was inseparable from protecting populations “because heritage enshrines people’s identities. It is a force for social cohesion and recovery. Protection of heritage must be an integral part of all humanitarian efforts.”

Some rebel groups now depend on smuggling antiquities to fund arms purchases. Many stolen items go to market in Amman, the Jordanian capital. “Every day we are getting calls about Syrian gold, Syrian mosaics, Syrian statues,” an antiques dealer told The Washington Post. “Damascus is being sold right here in Amman, piece by piece.”

Rebels are not solely to blame for heritage destruction; the army has also trained its artillery on monuments such as rebel-occupied Krak des Chevaliers. Abdulkarim has appealed to combatants on all sides to avoid archaeological sites, and Moushaweh says saving Syria’s monuments and antiquities requires a non-partisan message “addressed to all 23 million Syrians, without exception”.

Her ministry has driven a national advertising campaign, including billboards and leaflets, TV and radio spots and public meetings. It urges communities to take pride in and defend their cultural heritage. But appeals to national pride are unlikely to sway Islamic fundamentalists who are destroying statues, mosaics and icons they consider profane.

Abdulkarim describes the religiously motivated targeting of buildings and objects as “a new setback … adding to previous negative factors affecting the Syrian cultural heritage”. He cites damage to the imposing Byzantine basilica of St Simeon (pictured above) and the nearby second century al-Qatora stone statues carved into the sides of a valley. Armed bands are using both sites north of Aleppo as target practice, Abdulkarim says.

Another target is the ancient Christian village of Maloula, whose inhabitants still speak Aramaic, believed to have been the language of Jesus. An attack by Islamic fundamentalists last August caught villagers unawares as they prepared to celebrate the feast of the Exaltation of the Holy Cross. “Bodies have been left in the streets as a warning to the population,” the Catholic press agency AsiaNews reported.

Moushaweh, a Muslim brought up in a school run by Catholic nuns, says desecration of Maloula’s churches included the destruction of two “very significant” ancient icons and crosses that crowned the cupolas of monasteries pre-dating the arrival of Islam in the region.