Djibouti President Ismail Omar Guelleh seeks fourth term
Some observers say that this explains the muted criticism of President Guelleh from the West.
Polls opened at 0600 local time (0300 GMT), but voting got off to a slow start, the AFP news agency reports, with few of the country's 180,000 voters turning up early.
The result could be known as early as Friday evening, AFP says.
The opposition are angry that the president rescinded his earlier decision not to seek a fourth term.
His main rival, representing the opposition Union for National Salvation (USN) coalition, is Omar Elmi Kaireh, a Djibouti independence hero.
But another candidate, Mohamed Daoud Chehem, is from a USN splinter group, highlighting the fractured nature of the opposition.
Some other opposition parties are boycotting the poll.