Two days of artillery clashes have left many woundedSome 500 Somali fighters loyal to the last member of an alliance of warlords fighting Islamists in Mogadishu have surrendered, along with their weapons.
Abdi Qeybdid's forces had battled the Islamist militia for two days, leaving almost 100 dead and 200 wounded.
A BBC correspondent says the Union of Islamic Courts now controls 99% of the Somali capital and other key towns.
The Islamists deny claims made by the US and the weak, UN-backed government that they are linked to al-Qaeda.
Presidential palace
The BBC's Mohamed Olad Hassan in Mogadishu says the city is now quiet after two days of artillery exchanges and traffic is again able to move south from the capital.
One doctor said many more people may have died, with both sides burying their dead in the battle field.
Life under Islamist rule One of Mr Qeybdid's militia commanders, Sugule Ali Yusuf, told the BBC that his leader had escaped the city overnight but it is not clear where he has gone.
Some reports say Mr Qeybdid was injured and is hiding in a house in Mogadishu.
At least 30 of his battle-wagons, or technicals - open vehicles with anti-aircraft guns mounted on the back - were handed to the Union of Islamic Courts (UIC).
"They were holed up, in several buildings and we were pounding them with heavy artilleries and mortar from every corner, so there was no other option open for them but to surrender," said UIC gunman Abdi-Shakur.
Islamist fighters are moving from house to house around Mr Qeybdid's base, searching for any ammunition or weapons left inside the buildings.
Mr Qeybdid was a member of the Anti-Terror Alliance formed by the warlords who have controlled Mogadishu since the collapse of the last effective government in 1991.
The others members of the alliance, widely believed to have received US backing, have fled the city or surrendered to the UIC.
'Resistance is pointless'
One of the Islamist leaders, Sheikh Sharif Sheikh Ahmed, urged all gunmen not allied to the UIC to surrender their weapons.
"Any attempt to fight the Islamic courts is pointless. We are committed to put Mogadishu under one leadership," he said.
"Any group that tries to fight the Islamic courts will be destroyed. The Islamic courts have overcome the infidel stooges."
Some 38 'technicals' were handed over to the Islamic courtsOur reporter says just a few pockets of the city are now not in the hands of the Islamists.
Forces loyal to warlord Hussein Aideed still control areas near the presidential palace, Villa Somalia.
Mr Aideed, interior minister in the government, is not a member of the alliance and his gunmen only started fighting the Islamists over the weekend.
Observers believe the Islamists are now preparing an assault on the palace.
Somalia's neighbour Ethiopia is also alarmed by the Islamist advances - hundreds of troops and 70 trucks have reportedly crossed into Somali territory.
The UIC has made similar claims in the past and warned Ethiopia to withdraw.
Ethiopia has consistently denied that its troops have crossed the border.
Ethiopia is believed to support the government, based in Baidoa, 200km from Mogadishu.
On Monday, Prime Minister Ali Mohammed Ghedi told the BBC that his government would not hold direct talks with the UIC, accusing them of breaking a ceasefire agreement.
Peace talks were due to resume on Saturday in the Sudanese capital, Khartoum.
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