Ahmed Islam 'Madobe' was re-elected with 56 of 74 votes cast by regional MPs.
Ahmed Mohamed Islam 'Madobe' was officially sworn in on Thursday as president of Somalia’s federal state Jubbaland after winning a hotly-contested election.
Madobe won in the first round of voting garnering 56 votes of 74 votes cast by regional legislators in Kismayu.
His closest challenger, Anab Mohamed Dahir, got 17 vote while Mohamed Mohamud Omar came in third with one vote.
The poll was manned by African Union Mission in Somalia (Amisom) and Jubbaland security agencies.
Madobe, who has ruled over the Somalia state since 2013, was sworn in shortly after the electoral agency's chairman Dr Hamza Barre announced his victory.
He will serve for another for years.
However, the Federal government in Mogadishu had earlier said that the candidate selection process had violated the country's constitution and it would not recognise results by Jubbaland Independent Electoral and Boundaries Commission (JIEBC).
Meanwhile, in another poll held by a group opposed to Madobe, parallel legislators voted Abdirashid Hidig as president of Jubaland.
The move now throws the state into political uncertainty.
Ahead of the vote on Wednesday, UN representative in Somalia, James Swan had called on political players to refrain from violence.
“Whatever the outcome in Jubbaland tomorrow (Thursday), I implore all stakeholders to show restraint, refrain from violence, and resolve grievances through dialogue,” he told the UN Security Council in New York.
Mr Swan said international partners in Somalia were concerned about the absence of an agreed electoral process could trigger violence in southern Somali state.
“We are concerned that in the absence of such agreement, the likelihood of instability and division within Jubaland is significantly increased,” United Nations Assistance Mission in Somalia said in a statement.
—Additional reporting by Abdulkadir Khalif.