A recent agreement between Somalia's transitional government and the Islamic Courts may be put in jeopardy following Saturday's appointment of a hard-line cleric on the United States' most wanted list to head the courts.

Sheikh Hassan Dahir Aweys (File photo)

Sheikh Hassan Dahir Aweys is the leader of the Council of Islamic Courts, a new body that is to act as a kind of parliament for areas under the control of the Islamic Courts.

He replaces Sharif Sheikh Ahmed, who was seen by many to be a moderate and who was involved in last week's talks between the government and the Islamic Courts.

Analyst Richard Cornwell with the South African-based Institute for Security Studies says that Aweys' appointment and the re-structuring of the Islamic courts could reverse the gains in last week's talks.

"It now remains to be seen whether the agreements met with the transitional federal government in Sudan will be stuck to," he said. "They are meant to hold fresh talks beginning on the 15th of July. Whether this will happen now that the Islamic courts appear to be moving in the direction of setting up their own de facto administration I think is a very, very moot point."

Last Thursday, representatives of the Islamic courts, based in Mogadishu, and the transitional government, based in Baidoa, met with each other under the mediation of the Arab League.

The two sides agreed to recognize one another, cease hostilities, and hold more talks next month.

At the beginning of June, the Islamic courts took control of the capital Mogadishu and then Jowhar, a town that was once the temporary capital of Somalia's transitional government.

Much of southern Somalia appears to be under the control of the Islamic courts. It is not clear whether the Islamic courts will work with the fledgling transitional government, or set up an administration that would rival the government.

With Aweys' appointment, it is even less likely that the Islamic courts and the government, headed by Abdullahi Yusuf Ahmed, will work together.

Aweys and Mr. Yusuf are bitter enemies.

In the 1990s, Aweys headed the radical al-Itihaad al-Islamiyah group in the semi-autonomous region of Puntland. Al-Itihaad was believed to have links to al-Qaida, and with the backing of neighboring Ethiopia, President Yusuf led a successful campaign to crush the group.

Awyes is on record as saying the Yusuf government could not be supported because it is organized along secular lines.

Aweys is also on Washington's list of most wanted terrorists for his alleged links to the al-Qaida network. Many diplomats fear his appointment ushers in a Taleban-like safe haven for terrorists.

Since civil war broke out in 1991, warlords and their militias have battled with each other and civilians to control different parts of the country. A transitional Somali parliament was formed in Kenya more than a year ago following a two-year peace process.