Sheikh Sharif Ahmed (left) and Sheikh Yusuf Indohaadde during a news conference iin June 2006. Indohaadde, the former Defense Minister for the Islamic Courts Union, appeared on al Qaeda propaganda tapes.

Somalia’s newly expanded parliament elected the former leader of the Islamic Courts Union as president of Somalia. The move comes just days after the Djibouti wing of the Alliance for the Re-Liberation of Somalia joined in a power-sharing deal with the now-defunct Transitional Federal Government.

Sheikh Ahmed Sharif was elected president of Somalia in the second round of balloting held in the capital of neighboring Djibouti. Sharif received 293 of the 421 votes cast, while Masalah Mohamed Siad, the son of a former president of Somalia, received 126 votes. The current and a former prime minister of Somalia withdrew from the race after poor showings in the first round of voting.

The Somali parliament has been meeting in Djibouti as the security situation continues to deteriorate. The Ethiopian military, which has occupied southern Somalia since January 2006 after ousting the Islamic Courts, completed its withdrawal from Somalia this week.

Shabaab and allied Islamist groups from the Asmara wing of the Alliance for the Re-Liberation of Somalia have overrun most of southern Somalia, leaving small pockets under TFG control. Baidoa, the seat of government, fell to Shabaab forces on Jan. 26, the day after Ethiopian forces withdrew from the town.

The Alliance for the Re-Liberation of Somalia is an offshoot of the Islamic Courts Union, which took control of Somalia during the summer and fall of 2006. Sharif partnered with wanted al Qaeda leader Hassan Dahir Aweys during the 2006 conquest of central and southern Somalia, including the capital of Mogadishu. But Sharif has always been viewed as a “moderate” Islamist but the European Union and the US State Department, despite his close associations with al-Qaeda linked Somali leaders.

Under the leadership of Aweys and Sharif, the Islamic Courts Union implemented sharia, or Islamic law throughout southern Somalia. Islamic Courts suicide bombers attacked the weak Transitional Federal government, while the Islamic Courts ran terror training camps, courted foreign fighters, and released videos through al Qaeda’s propaganda arm. Aweys, confident in his victory, called for the creation of a “greater Somalia” in the horn of Africa.

“We will leave no stone unturned to integrate our Somali brothers in Kenya and Ethiopia and restore their freedom to live with their ancestors in Somalia,” Aweys said during an interview with Shabelle Radio in 2006.

Aweys and Sharif fled Somalia during the 2006 Ethiopian invasion. Aweys settled in Asmara, Eritrea, while Sharif was briefly imprisoned in Kenya. At the behest of the US State Department, Sharif was released from Kenyan custody and fled to Yemen and then Saudi Arabia. Aweys and Sharif established the Alliance for the Re-Liberation of Somalia and along with Shabaab launched the deadly insurgency that killed more than 16,000 Somalis in two years.

The two leaders split over the prospects of negotiations with the Transitional Federal Government. Sharif favored a power-sharing deal that would restore the Islamists to power, while Aweys sought to defeat the Ethiopian military and drive it from Somalia. Over the summer of 2008, Aweys claimed to have usurped the leadership of the ARS.

The extent of the divide between Aweys and Sharif is unclear. In early January, it was rumored the two leaders would meet in Egypt. With Shabaab and allied Islamist forces in control of nearly all of southern Somalia, it remains to be seen if Aweys and Sharif will reconcile or if the factions will continue to vie for political control of the war ravaged eastern African state.

Bill Roggio is a Senior Fellow at the Foundation for Defense of Democracies and the Editor of FDD's Long War Journal.

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