The nationalist Croat incumbent of Bosnia's tripartite presidency, Dragan Covic, has been defeated in elections by the more moderate Zeljko Komsic, the electoral commission says/
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Meanwhile, pro-Russia Serb separatist Milorad Dodik claimed victory over moderate incumbent Mladen Ivanic to take the Serbs' seat on the presidency.
Bosnia is run by a highly complex, multi-ethnic administration. Its tripartite presidency, the country's top executive and internationally representative body, is shared by one Bosnian Muslim, one Serb and one Croat.
The Muslim seat on the presidency was won by Sefik Dzaferovic, the electoral commission said.
Conceding defeat on Sunday, Covic warned of a "never-seen-before" crisis in the country, where hatred and mistrust between ethnic groups persists more than two decades after the Bosnian War ended.
Covic had campaigned on a promise of a greater autonomy for his compatriots along the lines of what the Serbs have.
Komsic however assured his supporters: "I will serve all citizens, even if they didn't vote for me."
But Dodik has stoked fears of fresh instability because he has pushed for Serbs to secede from greater Bosnia. He has also denied the genocide at Srebrenica and other atrocities committed in the war (1992-1995).
The West, which poured billions into reconstruction and attempted reconciliation, sees Dodik as the most destructive player in Bosnian politics. He has accused Western officials of meddling in the election.
The country's political system, with its exaggerated checks and balances, was imposed in 1995 as part of the US-brokered Dayton peace agreement, which put an end to the Bosnian War - but also left ethnic leaders with the authority to stop reforms and keep power in the hands of the political elite.
The country is also divided between two largely autonomous regions: the Serb-dominated Srpska Republic (RS) and the Federation of Bosnia and Herzegovina (FBiH), which is shared by Bosniaks and Croats.
Voters were on Sunday also electing the Bosnian parliament, as well as a president and parliament in the Srpska Republic and a parliament in the Federation of Bosnia and Herzegovina.
Results from those polls are not expected until later Monday, according to the electoral commission.
Australian Associated Press