Somali MPs late Monday chose academic Hassan Sheikh Mohamoud as the country's new President, upsetting the pre-election favourite and turning a major page in the search for a peace that has proved elusive for two decades.

It was a result that surprisingly ousted the old order, blamed for many of the ills afflicting the Horn of Africa country, including cronyism and rampant graft.

Prof Mohamoud decisively beat incumbent Sheikh Sharif Sheikh Ahmed in the second and final round, polling 190 votes of the 271 cast. Sheikh Ahmed received 79 votes with two ballots spoilt and immediately conceded the vote, shaking hands with the victor.

"I thank the Somali people, government officials, the army and the peacekeepers of the African Union Mission in Somalia (Amisom) for their collaboration during my tenure," he said in a concession speech that suggested that Somalis were ready for a fresh start.

The legislators were choosing the new leader after a number of obstacles including security concerns precluded the holding of a universal vote.

International community

The President-elect thanked the MPs for their strong faith in him after the vote held at the General Kahiye Police Academy and promised to work closely with the new Parliament.

"We want to initiate a new page for the Somali people,” said Prof Mohamoud, adding that he would spare no efforts in working to reintegrate Somalia back into the international community.

He will be in office for a four year-term.

Prof Mohamoud was one of the pioneers of educational development in Somalia after the collapse of the central government in 1991. He was one of the founders of SIMAD University, a higher learning institution based in Mogadishu, the capital.

He was the dean of the university until mid-2011 and has since then been leading an unregistered political organisation called the Peace and Development Party (PDP).

He had also been a civil society activist closely associated with a Mogadishu-based think tank, the Centre for Research and Dialogue (CRD).

During the campaign for the presidency, he co-found a political pressure group together other presidential hopefuls called ‘The National Partnership for Change.’

President-elect Mohamoud, 56, was born at Jalalaqsi district in Hiran region in Central Somalia and was educated in Somalia.

During a speech to parliament to outline his plans prior to the election, the academic indicated that peace, human rights and civil liberties would be his priority.

"Good governance is going to be extended to every region, district and villages,” he told the attentive legislators.

Roadmap ends

While thanking the outgoing president, Somalia's new leader acknowledged that his predecessors had made a lot of effort in realising many national dreams.

"I promise a continuation of all the achievements attained by my predecessors,” said Prof Mohamoud.

The election ended a process outlined in a roadmap that was meant to transform the eight-year transitional government into a permanent federal government.

The new government however inherits many problems.

Tough militants loyal to the Al-Qaeda-allied Al-Shabaab terror group are doggedly challenging the Somali Army and the AU peacekeepers propping up the Somali government.

Corruption remains rampant while the country embraces a federal system, a structure never tested in Somalia. The country's provisional constitution recently passed needs further polishing and a popular referendum for its approval.

Significantly, the first congratulatory message came from the leader of the semiautonomous Puntland State in north-eastern Somalia, Mr Abdurahman Mohamed Farole.

"As a young educated man, I trust that the new president will contribute to the stabilisation of Somalia," said Mr Farole, who had threatened to cut ties with Somalia if existing politicians who had run the country down were re-elected.

US reaction

The US also welcomed the vote, terming it "a crucial step forward".

"The United States calls on Somalia's leaders to usher in a new era of governance that is responsive, representative and accountable," White House spokesman Jay Carney said.

British prime minister David Cameron also welcomed the election of Prof Mohamoud.

But Al-Shabaab dismissed the ballot as illegitimate.

"The process in which Hassan Sheikh Mohamoud was chosen was run by the enemies of Somalia," Sheikh Ali Mohamud Rage, Shabaab spokesman, told news agency AFP.

"Nothing personal, but the whole process is like an enemy project," he said.