More than 13,000 polling places opened to accommodate the 7.1 million people eligible to vote. The election is one of dozens taking place Wednesday across Muslim-majority Indonesia.
Incumbent Gov. Basuki "Ahok" Tjahaja Purnama, a minority Christian and ethnic Chinese, is vying against Agus Harimurti Yudhoyono, who is the son of a former president, and Anies Rasyid Baswedan, a moderate now courting the votes of conservative and hard-line Muslims.
Religion and race, rather than the slew of problems that face a car-clogged and sinking Jakarta, have dominated the campaign and transformed the election into a high-stakes tussle between conservatives, who want Islam to be ascendant in politics and society, and moderates.
Hadiyul Umam, 40, a civil servant, said voting for Ahok would go against everything he believes in.
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"As a Muslim, I believe that non-Muslims are not allowed to lead Muslims in this country, and personally, I do not like the way Ahok leads, which is not pro-poor people and his words were disrespectful and rude," he said.
Ahok's blasphemy trial and the ease with which hard-liners attracted several hundred thousand to protest against him in Jakarta have undermined Indonesia's reputation for practicing a moderate form of Islam and shaken the centrist government of President Joko "Jokowi" Widodo.
Defeat for Ahok would also be a defeat for Indonesia's moderate political and religious leaders and further embolden hard-liners, who say a non-Muslim should not lead Muslims. The governorship is also seen as a launching pad into national politics and possibly the presidency.
Jokowi voted in a neighborhood of central Jakarta and called for unity.
"Differences of political choice should not to divide us," he said. "After this election, we want everything to be back as brothers, we all need to maintain our unity and integrity.