Thursday's march was the latest protest since the Islamic courts militia defeated US-backed regional commanders earlier this month.
About 700 protesters, including children from Quranic schools, marched for three hours through the capital's streets in the central Sinai district in a demonstration organised by the traditional Sufist group, Ahlu Suna Wal-Jammaa.
"We are Muslims and we do not want these fundamentalists who seized Mogadishu," said Muumina Ali, a demonstrator.
"Sheikh Sharif's group are fundamentalists," shouted another protester, referring to Sheikh Sharif Sheikh Ahmed, chairman of the Islamic Courts Union (ICU) which controls Mogadishu and other towns across a swathe of southern Somalia.
The protest comes as Somalia's interim government and the Islamist movement are holding direct high-level talks in Sudan, mediated by the Arab League and the Sudanese president.
'Taliban' claims denied
While the ICU has brought relative peace and stability to Mogadishu for the first time in years, residents say some Islamist militia are imposing hardline practices, such as forcibly cutting hair and making women cover their heads and faces.
Ahmed, the moderate face of the ICU which also includes more radical Muslim leaders, has denied accusations that his organisation wants to establish a Taliban-style rule in Somalia.
There have been earlier protests
against the Islamists' victory
The Islamist takeover of Mogadishu has complicated the attempts to restore central rule to Somalia since the 1991 removal of the president, Mohamed Siad Barre.
A weak interim government, formed in Kenya in 2004, is based in the provincial town of Baidoa.
However, it retains little control over the rest of the country, including the capital.
Abdullahi Yusuf, Somalia's interim president, said this week the Islamist militia could not have succeeded without support from Muslim fundamentalists across the world.
But the ICU says the government was formed without the consent or consultation of the Somali people and is conspiring with Ethiopia to attack them.
Thursday's march followed other anti-Islamist protests, including one organised by a defeated commander and another by people protesting over the breaking up of World Cup viewing in some cinemas.
The ICU said it was preparing a massive demonstration for Friday in Mogadishu to show the superior popular support it has and the people's opposition to a government plan to invite foreign peacekeepers into Somalia.