Polling is taking place amid allegations of irregularities and vote officials say voting may be extended.
The president faces five challengers, some of whom have criticised his "dictatorial and bullying" style.
President Gayoom is Asia's longest serving leader, having been in power for more than 30 years.
His main challenger to the presidency, Mohamed Nasheed, said that although there were cases of voting lists not matching official records, the irregularities were minor and he feared violence if the vote was not completed. read more BBC News