Polls began to close at 5 p.m. (1600 GMT), though many continued to vote after a day that passed without violence.
Authorities had repeatedly delayed the elections, not least due to violence in the capital Bangui in September, and some people doubt militia groups at the heart of the conflict will accept the result if it goes against them.
Thirty candidates are competing in the presidential election, a major milestone in the transition to democracy, while all National Assembly seats are being contested.
Interim President Catherine Samba-Panza, who held office since May 2014, is barred from standing. In the absence of opinion polls it is difficult to predict the winner.
Earlier, queues formed at polling stations in Bangui and in the mainly Muslim PK-5 neighborhood. United Nations peacekeepers positioned armored personnel carriers at voting stations, witnesses said, after gunmen attacked voters in the capital and elsewhere during a referendum on the new constitution this month.
About one million people from a population of 5 million have been driven from their homes by fighting and campaigns of ethnic and religious cleansing.
"I've been dreaming of this election for two years since the day armed men killed my father and my brother in Bangui. I voted for peace," said Ahmat Abouna, who fled to the Cameroon border town of Garoua-Boulai and voted along with thousands of other refugees.
The election authority said it would rerun voting for the National Assembly in some areas because ballot papers failed to arrive. No date for the re-run was set.
TALK OF SECESSION
Mainly Muslim rebels from a group called the Seleka seized power in the majority Christian nation in early 2013, provoking reprisals from Christian anti-balaka militias. Leaders have since fueled a cycle of religious and inter-communal killings.
Leading presidential candidates include former prime ministers Anicet-Georges Dologuele and Martin Ziguele, who received a boost on Tuesday when anti-balaka militias who have formed the Central African Party of Unity and Development said they would support his candidacy. Other candidates include former Foreign Minister Karim Meckassoua and Bilal Desire Nzanga-Kolingba, the son of a former president.
"All the candidates are on the same footing. The outgoing president has not supported anyone," said Ziguele as he voted.
The Seleka withdrew from Bangui after their leader Michel Djotodia stepped down from the presidency in 2014 and the group's factions have entrenched themselves in the northeast, leaving the country effectively partitioned.
Some have flirted with secession and convincing them to cede control may not be easy if the new president is deemed a threat to Muslims. The new president must also disarm militias.
The economy has struggled for years, with uranium deposits undeveloped, the cotton sector in trouble and gold and diamond mines under the control of militias.
Provisional results will be announced in the following days and the constitutional court must give final results 15 days after polling day.
Central African Republic votes, aiming to end violence
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