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The cleric, Sheik Sharif Sheik Ahmed, headed the Islamic courts movement that governed the capital, Mogadishu, and most of southern Somalia until 2006. Some analysts had said they thought that Sheik Sharif had the best chance of all the candidates for president to unite Somalis, because of his Islamist roots and his acceptability to a variety of factions.
Parliament was selecting a replacement for the former president, Abdullahi Yusuf Ahmed, who resigned in late December after four years in office. A former warlord, Mr. Yusuf had been widely blamed for Somalia’s deepening crisis and had been steadily marginalized.
The lawmakers broke into applause when Sheik Sharif reached the minimum number of votes needed for victory, 213, a little before 4 a.m. during an all-night session of Parliament. The legislators were meeting in Djibouti, just north of Somalia, under a United Nations-brokered deal to establish a unity government between the transitional government and moderate Islamists.
“I promise that I will serve my people loyally and neutrally without color or clan,” Sheik Sharif told the lawmakers after the balloting. “I call other Somalis who are not part of this peace process to join us.”
He defeated Gen. Maslah Mohamed Siad, the son of the former dictator, Maj. Gen. Mohammed Siad Barre, in the second round of voting. The outcome seemed likely after Prime Minister Nur Hassan Hussein withdrew from the balloting after the first round. He had been considered Sheik Sharif’s main rival for the presidency, but he withdrew after winning only 59 votes in the initial round.
In Mogadishu, where many people stayed up all night to follow the election on radio and television, people celebrated in the streets immediately afterward, with shots being fired into the air.
For Sheik Sharif, the burden of reconciling Somalia’s 10 million people and ending 18 years of bloodshed will be daunting. Most of Somalia is controlled by various Islamist militias, although some of the moderate Islamist groups support the government. The government itself controls only a few blocks of Mogadishu.
The Shabab, a hard-line Islamist militia, controls most of Mogadishu and much of the southern part of the country. It has denounced the election in Djibouti as meaningless, and on Monday captured the seat of Parliament in the town of Baidoa.
Somalia has been without a functioning central government since 1991, when General Siad Barre was removed from power and the army fell into the hands of clan militias, who turned on one another and left the country largely in anarchy.
