Queues formed early at polling stations in downtown Podgorica, the provincial-looking capital of the mountainous state, with elderly men dressed in their Sunday best filling in the pink voting slips which ask simply: "Do you want Montenegro to be an independent state?" Answer yes or no.
There was little doubt in the run-up to the ballot that the pro-independence camp would emerge stronger by the time polls close at 9pm (1900 GMT), but the question is whether it can muster the 55% majority needed for a clear win.
The union of Serbia-Montenegro, the last vestige of the former Yugoslavia, was created in 2003, but the two southern Slav cousins have been together in some form of joint state for almost a century.
Montenegro's government says independence will open the way to economic prosperity in the European Union. Those in favour of keeping the union with Serbia say the country of 650,000 is too small for a risky venture in going it alone.
"We will know by midnight (2200 GMT)," said Marko Blagojevic of the Centre for Free Elections and Democracy which plans to project the result from a sample of 300 out of 1,120 polling stations.
The referendum commission said it would not declare the outcome before Monday morning at the earliest.
Even before voting began, supporters of independence were setting off fireworks and roaring around the capital on Saturday night with their car horns blaring.
The national flag, banner of their campaign, was draped from hundreds of balconies.
Serbia-Montenegro was created with the mediation of the European Union, which was afraid of further fragmentation in the Balkans.
Before that, the two neighbours were together in two monarchies, in Josip Broz Tito's Yugoslavia and in the Yugoslav federation of late Serbian leader Slobodan Milosevic.
Serbia has asked Montenegrins
to vote for preserving the union
Serbia is the dominant partner in the union with 7.5 million people and an economy 10 times bigger than Montenegro's. It has called on Montenegrins to vote for preserving the union.
Pro-unionists uphold the long historical and cultural link with Serbia and say Montenegro needs the jobs, education and health care their larger neighbour can provide.
The EU this month froze talks on closer ties over Belgrade's failure to arrest fugitive war crimes suspect Ratko Mladic - another argument used by the independence camp in favour of separation.
Analysts see few practical effects from a divorce. The two republics already have different laws, economic policy and currencies, sharing only five ministries that supervise defence, diplomacy and minority rights. Their joint parliament barely meets.
Most ethnic Montenegrins, 43% of the population, were expected to choose independence, as were Muslims, ethnic Albanians and other minorities. The 32% ethnic Serbs are overwhelmingly for preserving the union.
Despite high emotion, the run-up to the referendum was uneventful. Security forces expected no trouble on polling day.
Some 3,400 monitors from Montenegro and abroad were due to scrutinise the voting for irregularities - a ratio the EU says is high enough to ward off fraud allegations common in past elections.