Petru Luchinsky, 54, a member of former president Mikhail Gorbachev's politburo, won by 57 to 43 in a secret ballot in the 104-seat legislature, according to results announced in the chamber.
Luchinsky's Agrarian Democratic Party won an overall majority of 56 seats in last month's election, the first since Moldova won its independence from Moscow in 1992.
The party, supported by the powerful farming lobby, favors independence rather than a merger with neighboring Romania or restoration of the Soviet Union.
A powerful political personality, Luchinsky is regarded as a potential rival to President Mircea Snegur.
But political analysts in Kishinyov said some Agrarian Democrat members, suspicious of his ambitions, might have voted against him.
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