While many of the brigades involved in the fighting are decidedly Islamist in outlook and some have boasted about executing captured soldiers, two of the most extreme groups fighting in Syria were not invited to the rebel meeting in Turkey or included in the new council — a move that could encourage Western support.
Disorganisation has bedeviled Syria's rebel movement since its birth late last year, when some protesters gave up on peaceful means to bring down President Bashar al-Assad's regime and took up arms, forming the base of what became the Free Syrian Army.
But the movement has never actually been an army. Scores of rebel groups battle Assad's forces across the country, many coordinating with no one outside of their own area. While some say they want a civil, democratic government, others advocate an Islamic state.
The new body, expected to be announced officially on Sunday, hopes to form the basis of a united rebel front.
Some 500 delegates elected the 30-person Supreme Military Council and a Chief of Staff on Friday and planned to meet soon with representatives from the opposition's newly reorganised political leadership, participants said.
"The aim of this meeting was to unify the armed opposition to bring down the regime," said a rebel commander from near Damascus who attended the meeting. "It also aims to get the situation under control once the regime falls."
The move toward greater unity on the armed front comes as the US and others try to strengthen the opposition's leadership while sidelining extremist factions that have become a vital part of the rebels' ground forces.
The opposition's political leadership reorganised last month, under Western pressure, into a new National Alliance that its backers hope will have broader representation and stronger links to rebel fighters.
Britain, France, Turkey and several Gulf Arab nations have recognised the National Alliance, effectively considering it a government in exile.
The US is expected to recognise it at an international "Friends of Syria" conference in Marakesh, Morocco, that begins on Wednesday.
It remains unclear how the new military command will relate to the National Alliance and whether foreign powers will back it.
But two of Syria's most extreme rebel groups were not included: Jabhat al-Nusra, which has claimed deadly suicide bombings and is believed to be linked to al-Qaeda, and Ahrar al-Sham, an Islamic fundamentalist brigade home to many foreign jihadis.
US officials have said the Obama administration is preparing to designate Jabhat al-Nusra a terrorist organisation.
Many of the participating groups have strong Islamist agendas, and some have fought in ways that could scare away Western backers. They include the Tawheed Brigade, whose ideology is similar to that of the Muslim Brotherhood, and the Falcons of Damascus, an ultraconservative Islamist group. Its leader, Ahmed Eissa al-Sheik, told the Associated Press earlier this year that his men had executed five captured government soldiers.
Elizabeth O'Bagy, who studies Syria's rebels for the Institute for the Study of War, said the new command included important on-the-ground commanders, which will give it more support from various rebel factions. The inclusion less extreme Islamist brigades will also give the body credibility.
"They are going to have a role in a future Syria and sidelining them will only fuel tensions," she said. Including them "shows that this command is representative of those on the ground, not just the ideal candidates for the West".
If the new command can lead effectively and supply badly needed weapons, it could attract fighters who joined hard-line groups because they were flush with arms but may not agree with their ideology, she said.
A rebel official said more than 500 delegates had been meeting since Wednesday in the Turkish resort of Antalya and were planning to announce their new group on Sunday.
The rebel commander from near Damascus said the group had chosen Brigadier-General Salim Idriss, who defected from Assad's army, as its chief of staff. It also had divided Syria into five regions, each of which will be under one of Idriss' assistants.
The new structure diminishes the role of previous leaders in the Free Syrian Army. Brigadier-General Mustafa al-Sheikh, who headed the FSA's Military Council, will play no rule in the new structure, the commander said. Riad al-Asaad, the head of the Free Syrian Army, will retain a symbolic post.
The official and commander spoke on condition of anonymity because they were not authorised to discuss the meeting before its conclusion.
The Syrian government did not comment on the new rebel command and throughout the uprising has considered the rebels terrorists backed by foreign powers that seek to destroy the country.
Assad's regime appears increasingly embattled, with rebels making gains in northern Syria and near Damascus while the US, Turkey and others seek to hasten its demise. US officials have expressed fears that Assad could use chemical or biological weapons, and US intelligence has reported new activities at sites housing Syria's chemical weapons.
The government tried to reverse the charge on Saturday, saying it had warned the United Nations that "terrorist groups" might use chemical weapons.
Syria's state news agency said the Foreign Ministry had sent letters to the UN Security Council and UN chief Ban Ki-moon saying that Syria would not use chemical weapons against its own people.
Syria has never confirmed it has chemical weapons, but outside experts believe it has substantial stockpiles of mustard gas and a range of nerve agents, including sarin, a highly toxic substance that can suffocate its victims by paralyzing their lungs.
No rebel groups are known to possess chemical weapons and it is unlikely their mostly amateur fighters would know how to use them.
Anti-regime activist say more than 40 000 people have been killed since Syria's uprising started in March 2011. – AP