Polling stations closed at 4:00 p.m. local time (08:00 GMT) in the self-governed province, which China considers to be part of its territory.
The front-runner in the presidential race is Ma Ying-jeou of the opposition Nationalist Party, which favors eventual reunification with China. The province split from the mainland following the 1949 Civil War.
The ruling Democratic Progressive Party led by Frank Hsieh is seeking formal independence from Beijing, but like Ma, former premier Hsieh wants closer economic ties with China.
Outgoing President Chen Shui-bian's pro-independence stance has sparked tensions with Beijing.
Around 75% of the 17 million Taiwanese eligible to vote took part in the election.
The final results will be announced at 9:30 p.m. Taipei time (13:30 GMT).
