The Islamic alliance, which ousted US-backed warlords from the Somali capital after four months of fighting, said it was attending the talks with no preconditions.
"The sole aim is making them a success," said delegation head Ali Mohammed Ibrahim.
Somalia’s government sent a team headed by the president, the prime minister and the speaker of parliament to the talks which are being held in the Sudanese capital, Khartoum.
Sudan hosts talks
Sudanese President Omar al-Beshir, the current chairman of the Arab League, offered to host the talks between Somalia's transitional government and the Islamist union, known as the Joint Islamic Courts.
The Joint Islamic Courts militia has overrun much of southern Somalia and has vowed to re-establish order and begun imposing Sharia Islamic law in the areas it controls.
It rejects accusations that is has links with extremists, including Al-Qaeda.
"We do not know the agenda yet but we believe it has something to do with the restoration of peace and stability that we are also trying to bring in Somalia," said he leader of the Islamic union, Sheikh Shariff Sheikh Ahmed.
He said the Islamists had already restored order to parts of the country under their control.
Somalia's transitional authority, which sits in Baidoa, west of
Mogadishu, because of fears of attacks in the capital, has little real hold over most of Somalia. It accuses the Islamists of plotting to overrun the whole country.
It is unclear how effective the Khartoum peace talks will be since both sides have so far refused to compromise.
US seeks Islamists help
Meanwhile in Nairobi, a high ranking US diplomat for Africa, Jendayi Frazer, has sought the help of the Joint Islamic Courts to arrest terrorists believed hiding in Somalia.
Washington previously blamed these courts for having links with Al-Qaeda and harbouring foreign fighters and asked warlords as well as the Somali government to help arrest them, but in vain.
"We are making the same call on the Islamic Courts Union, we need to work with all elements," Frazer said in Nairobi.
"They need to come together in a dialogue so that they can create a place in which terrorists cannot have a safe haven. We will keep working with the Somali people and I am absolutely convinced that they want us to be there working with them."