Around 93% of voters in Crimea have backed joining Russia and seceding from Ukraine, according to exit polls quoted by Russian news agencies.
Polls closed at 18:00 GMT and officials hailed a "record" turnout. Preliminary results are expected within hours.
Many opponents boycotted the vote, which has been rejected by the US and the EU as illegitimate.
Pro-Russian forces took control of Crimea in February after Ukraine's pro-Moscow president was overthrown.
On the ballot paper, voters were asked whether they would like Crimea to rejoin Russia.
A second question asked whether Ukraine should return to its status under the 1992 constitution, which would give the region much greater autonomy.
There was no option for those who wanted the constitutional situation to remain unchanged.
Ethnic Russians make up 58.5% of the region's population, and many of them were expected to vote for joining Russia.
There are 1.5 million eligible voters.
Sergei Aksyonov, who was installed as Crimea's regional government leader after Russia's military takeover, said the people had voted freely.
"There are no problems at polling stations. I don't feel or see that any pressure is being applied," he told Interfax news agency.
One voter, Olga Koziko, told the BBC that she was voting for secession because she did not want to be governed by "those Nazis who came to power in Kiev".
"Russia will defend us and protect us," the schoolteacher said.
Away from the Crimea region, unrest continued in the south-east Ukrainian city of Donetsk.
Pro-Russian protesters stormed the prosecutor's building shouting "Donetsk is a Russian city", and then broke into the local security services headquarters for the second time in two days.
They later dispersed but promised to return on Monday.
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