The key post is for the next mayor of Chisinau, the capital, where pro-European incumbent Dorin Chirtoaca faces pro-Russian challenger Zinaida Greceanai, a former prime minister of the Communist Party.
A low turnout in the city of one million will benefit the 59-year-old Greceanai.
"I hope we will clarify things.... and build something that is certain, definitive, irreversible, for the future of Chisinau and Moldova," Chirtoaca said after voting.
"Residents have a great desire to see deeds and not just statements," said Greceanai.