IT IS the shoes of the murdered bus passengers that everyone remembers. Nine corpses, nine sets of footwear — a girl’s plastic sandals, a boy’s trainers and clean white socks, a woman’s sensible casuals — all lined up by the jungle roadside.

The scene marked another grim milestone in an insurgency that has torn apart Thailand’s three majority Muslim provinces for the past three years.

First, the attackers threw a grenade to stop the minibus. Then they shot dead the passengers, one by one. Only the driver survived. The executioners heard him gabbling to Allah for forgiveness, realised he was not a Buddhist and spared him.

After that, communal passions erupted. Crowds of Muslims and Buddhists took to the streets to demand protection. Since the ambush a string of killings claiming victims of both faiths has taken the death toll to more than 2,100.

The insurgency is now the bloodiest conflict in southeast Asia. Yet it is a war of shadows. The militants issue no communi-qués. They have no known leaders. They have made no precise demands. If they are connected to the worldwide network of Al-Qaeda and its affiliates there is no proof.

There is a sense of siege over the hushed towns and quiet fishing villages in the palmy jungles of the far south of Thailand.

Nearly 100 years ago Siam absorbed the provinces of Pattani, Yala and Narathiwat, then Islamic sultanates, in a treaty brokered by the British colonial rulers of Malaya. Sporadic resistance has broken out ever since.

The latest insurgents borrow political and military techniques from Iraq and Lebanon. Their favoured method is the drive-by assassination by a pillion-riding gunman on a motorbike. They also slit throats and cut off heads as examples.

One officer in Thai military intelligence shows visitors photographs recording the eviscerated bodies of Buddhist monks, images so stark that they have been kept out of the Thai press for fear of igniting a pogrom.

De facto ethnic cleansing is already in progress. When the Thai-Chinese community celebrated the year of the pig, a feast calculated to incite loathing for the infidels, militants unleashed 50 bomb and arson attacks on their businesses. The targets included a large rubber factory that lost more than £5m of stock.

Many Chinese are planning to sell up and go. But Ah Seng, an elderly Chinese herbalist living with his wizened wife in an open-fronted wooden shop-house, laughed at the thought that he would ever leave.

“Children, grandchildren, all here, this is always our home,” he said, sweeping his hand around an array of family photographs and altars to assorted deities, over which there reigned a portrait of Thailand’s revered King Bhumibol Adulyadej.

His neighbours were Muslims who were counting their stocks in a cool wooden warehouse where sheets of raw rubber were stacked just as they were a century ago.

“Who wants fighting? Only the troublemakers,” said the owner, who did not want to be identified. “Thank God it is quiet here.”

Quiet it was. But moored by the customs house were two Thai gunboats whose crews had strewn their bedding on the foredecks so as to sleep around the .50calibre machineguns.

Thai officials scurry around in armoured vehicles. Sandbags and barbed wire protect key locations. Troops and police run patrols to try to reassure people, without success.

“Even a Muslim like me is better off back in the city and off the roads by 3pm,” said the manager of a hotel in which I was the only guest. “And I do not advise you as a foreigner to go out after dark.”

Yet statistics show that almost half the victims are Muslim. This is also a war within a war to dominate the Islamic community. Moderates risk threats and ostracism. Informers and collaborators with the Thai state are doomed.

Three schoolboys died the other week when grenades were thrown into their playground. The message, say analysts, is: Muslim youth should get out of schools run by the Thai government and attend private Islamic foundations often run by Thais trained in the Middle East.

Then there are the government’s “dirty war” tactics that have claimed Muslim victims. Somchai Neelaphaijit, a prominent lawyer, vanished at the hands of the police and is believed to be dead. This month Human Rights Watch said the security forces were implicated in 22 disappearances.

Surayud Chulanont, the prime minister, has pledged no more abuses and promised more rights to Thailand’s 4m Muslims, out of its 65m population. But the rate of killing has tripled to about four deaths a day since his junta seized power in Bangkok last year, pledging a “new start” in the south.

The government has not only lost control of the political agenda. It is also failing to keep the initiative on the battlefield, despite deploying 30,000 troops.

One example: in striving to stop the use of roadside bombs triggered by mobile phones, the security forces blocked the networks. Only Thais who have registered their ID cards with the military can use a mobile.

The insurgents quickly switched to digital watches or infrared devices to detonate the bombs. They also increased the average size of their explosive devices from 4½lb to more than 9lb. Some bombs pack 33lb. Not one bomb-maker has been identified by army forensic teams.

“The coup leaders continue to ask the wrong questions and refuse to take the conflict for what it is — an Islamic insurgency,” said Professor Zachary Abuza of Simmons College, Boston, the leading foreign expert on the struggle. “Many Thais think it’s only about poverty and social justice,” he added.

Abuza says that two well established separatist groups, the National Revolutionary Front and the Pattani Islamic Mujaheddin Movement, are the prime movers.

Intelligence officers from Thailand and its allies are not wholly convinced. Interrogations have produced stories of tall, hooded terrorist trainers who are not Thai. Eavesdroppers have picked up radio chatter in Indonesian.

There remains little or no documentary evidence of global links, although a lone Arabic website has made its debut extolling the jihad in southern Thailand. Perhaps the greatest mystery is why the militants have stayed on their home ground, refraining from attacks on Thailand’s multi-billion-pound tourist industry.

In an ominous development, however, military intelligence officers recently disclosed that they had picked up two surveillance teams of suspected extremists in Bangkok and Phuket within the past 18 months.

“This is a downward spiral,” said Abuza, “and it could be just a matter of time.”

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