Former coup leader Azali Assoumani won last month's run-off vote by just 2,100 votes, according to provisional results, but a court ordered 13 polling stations on Anjouan island to vote again due to "irregularities".
Polls closed at 1500 GMT and voting passed off without any major incidents, according to an AFP journalist.
Just 6,305 voters were called to vote today, two per cent of the Comoros electorate. The results could be known as early as Wednesday night while the inauguration of the winner is scheduled for May 26.
Turnout was high today, with hundreds of people waiting in line during the day as armed security forces stood guard to ensure voting was smooth.
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"We did not vote last time but today the military are protecting me and my blind husband," Boueni Aboudou told AFP.
The army deployed 200 soldiers in Anjouan, according to the country's Chief of Staff Youssouf Idjihadi.
In Mramani in the south, where voting had to be discontinued last month after a crush of voters, as many as 100 armed soldiers stood guard outside five polling stations located in a school, according to an AFP journalist.
Soilihi, who is known as Mamadou, said he rejected the provisional result.
Assoumani first came to power in 1999 after ousting acting president Tadjidine Ben Said Massounde in a coup.