While some Somalis - and certainly the US - are deeply dismayed at the sight of the Islamic militia seizing control of Mogadishu, others argue that it may prove it to be a turning point in the peace process.
The Islamic courts are supported by many in Mogadishu
Prime Minister Ali Mohamed Ghedi says he would rather deal with the Union of Islamic Courts than the warlords who have controlled Somali's capital for the past 15 years.
"It was an excellent step forward... because they [warlords] were not ready for a government, they were not ready for peace," he told Radio France Internationale.
Mr Ghedi's transitional government was set up after two years of sometimes tortuous peace talks in neighbouring Kenya between all of Somalia's different clans and armed groups.
Great care was taken to ensure that all sides were represented.
As a result, the Mogadishu warlords were all named as ministers even though many did not really believe in the government.
Optimists say that if the Islamic courts do consolidate their grip on the capital, negotiations between just two groups may prove simpler, leading to the country's first effective national authority for 15 years.
Islamist leader Sharif Sheikh Ahmed and Mr Ghedi, based in Baidoa, 250km (155 miles) north-west of the capital, have both said they are ready for dialogue.
Editor of the BBC Somali service Yusuf Garaad Omar says the fact that a single entity controls the capital is a huge opportunity to bring peace to Somalia.
"The Islamic courts and the transitional government need each other," he says.
"One is the legal government, the other is a popular force in control of the capital."
But he warns that it is only a step forward on a long road towards the end of war.
He says the Islamic courts are likely to become whatever others want them to be.
If treated with respect - as partners - they could turn into the group which delivers the capital to the government and so end years of conflict.
But if they are viewed as a hotbed of Islamic extremism, that too, could become a self-fulfilling prophecy.
The moderate leader of the Islamic Courts Union, Sharif Shaikh Ahmed, has said that his militia does not want to impose a Taliban-style Islamic state on Somalia.
But some Islamic courts officials have said they would only support a government based on Islam.
Furthermore, President Abdullahi Yusuf fought a successful campaign against a previous Somali Islamist armed group, al-Itihaad al-Islamiya, when he was in charge of the northern region of Puntland.
Sheikh Aweys' forces were beaten by President Yusuf in the 1990s
Al-Itihaad al-Islamiya leader Sheik Hassan Dahir Aweys is a key figure in the Islamic courts.
Mr Aweys has said he has nothing against Mr Yusuf personally but this history could make negotiations difficult.
President Yusuf condemned the US for allegedly backing the warlords against the Islamic courts.
But he did not say it was morally wrong - just that the money should be channelled through his government instead.
Mr Ahmed has said he wants an end to the fighting, which has killed at least 350 in the past few weeks.
But there are reports that his militias are advancing on Jowhar, where some warlords have fled.
Fresh from what seems to be a comprehensive victory in Mogadishu, the Islamic courts might seek to achieve what no other group has managed since 1991 - to conquer the whole country.
President Yusuf was last year trying to build up a new national army and may command the loyalty of gunmen from Puntland.
However, US-based Somali analyst Omar Jamal says the Islamic court could defeat government forces, if they so wished.
"If the Islamic leaders want, they could kick the government out of Baidoa very easily - not only on military grounds, but also on political grounds, the government is so weak, the Islamic extremists are far ahead in gaining the hearts and minds of the people," he told the AP news agency.
"This war will not stop in Mogadishu."
Another possibility, just as bleak, would be that the US is so concerned that the Islamic courts were harbouring al-Qaeda elements that they hugely increased their support for whichever group promised to fight them.
This would only prolong the instability that most Somalis are desperate to put behind them.