A total of 1,020 polling stations opened across the country at 0800 hours and were due to close at 2100 hours. The voting will be overseen by more than 3,500 monitors, nearly 700 of them from abroad.
Montenegro will become independent if 55 per cent of the votes cast are in favour, a rule set by the European Union in order for the ballot to be valid.
The pro-independence bloc is headed by the ruling Democratic Socialist Party of Prime Minister Milo Djukanovic, while the unionist bloc is led by Predrag Bulatovic of the largest opposition Socialist People's Party.
Both sides are convinced of victory. Analysts give a slight edge to the pro-independence camp.
The central electoral commission has said that the results of the vote will be announced on Monday, while the Centre for Democratic Transition has said it will make preliminary returns public half an hour after the closure of the polling stations.