Both the ruling and main opposition parties have proposed plebiscites asking voters if Taiwan should enter the United Nations.
Besides ballots for the presidential candidates, polling stations also provided ballots and boxes for each referendum.
"There's no real significance to the referenda. Even if they do pass that won't lead to our getting into the U.N.," said Taipei voter Lee Yung-chou, 39, after emerging from a polling station.
Taiwan held a U.N. seat until 1971, when it was taken by China, which has since thwarted the island's every move to rejoin the world body. Beijing has veto power as a permanent U.N. Security Council member.
"Of course, we all want to return to the U.N., but this is impractical. It's a waste of resources," Lee said.
The ruling Democratic Progressive Party proposed a referendum asking voters if the island should enter the United Nations under the name "Taiwan."
Since the early 1990s, Taiwan has applied to rejoin the United Nations under its official name "Republic of China."
Last year, for the first time, the island applied -- again unsuccessfully -- for U.N. membership as "Taiwan" in an assertion of sovereignty that China has slammed as "provocative."
China views Taiwan as a breakaway province awaiting unification, by force if necessary.
The DPP referendum has also created friction in Taiwan's relations with the United States, which seeks to rein in moves by Taipei to formalize the island's de facto sovereignty for fear of provoking Beijing and sparking a war that could involve Washington, Taiwan's chief security guarantor.
Politically, the DPP's referendum is designed to give extra incentive to supporters to head to polls and vote for its presidential candidate Frank Hsieh.
Hsieh is in a tight race against Ma Ying-jeou of the KMT, which also proposed a "U.N. referendum" in reaction to that of the DPP.
The KMT referendum asked voters if Taiwan should return to the United Nations under the title ROC or any other appropriate name that upholds the island's "dignity."
The DPP officially supports both questions, while the KMT has boycotted the DPP's, citing what it says is a bid by the ruling party to influence the election's outcome via the plebiscite.
"Taiwan is small, but it's a nation, and there's no reason why we shouldn't have some international space for ourselves," said one Taipei voter, identifying herself only by her surname Mai.
"Taiwan has to fight for itself and send a message to the world," Mai, a 25-year-old nurse, said after casting ballots for both referendums.
"About half of registered voters in the area have cast ballots for both referenda," said a Taipei polling station volunteer at 2 p.m., two hours before the polls closed.
"It seems young people are casting ballots for the referenda, while older voters are boycotting them," said another volunteer.
Neither referendum is likely to pass, however, because of high required thresholds of acceptance and the KMT boycott.
In Taiwan, a referendum requires the participation of more than 8.5 million registered voters, half the electorate, to be valid, and requires the support of more than 4.25 million of them to pass.