Ciubotea is seen as a modernizer within the church, but his reputation has been tainted with accusations that he had ties to the country's communist-era secret police.
Ciubotea, who becomes the sixth patriarch of the Romanian Orthodox Church, expressed his gratitude to the Holy Synod upon his election. "We only want to thank the Holy Synod and the members of the Electoral Religious Commission for the trust they put in me," he said.
The Holy Synod chose Ciubotea from three candidates: Ciubotea, Cluj Archbishop Bartolomeu Anania, and the bishop of Covasna and Harghita, Ioan Selejan. The three were narrowed down from the initial pool of 30 high-ranking members of the clergy.
Ciubotea had been serving as the interim patriarch after the death of the previous Patriarch, Teoctist, in late July 2007.
Western Education, Suspicious Background
Western-educated Ciubotea is known as a "modernist" who has supported reforms and has been open toward the ecumenical movement. He has also angered many traditional monasteries in Romania's eastern region of Moldavia.
Ciubotea spent a long time in the West, studying theology and working in various Catholic and Protestant institutions.
But it is that background that has cast a shadow on Ciubotea's reputation. Many in Romania have said he was allowed to live abroad because of his collaboration with Romania's feared secret police, the Securitate.
Mircea Dinescu, a representative of the Romanian national council that studies the Securitate archives, recently announced that the council knows of a group of top Orthodox clerics who had collaborated with the secret police. Dinescu did not disclose any names, but media reports have said that Ciubotea was one of those implicated.
The council invited two of the candidates, Ciubotea and Anania, for an interview, but they refused.
After the elections, the council today announced that it might fully disclose its findings about collaboration between the clergy and the secret police.
Ciubotea wasn't the only candidate who was suspected of having a murky history.
Similar accusations were also made toward the 86-year-old Anania.
From 1965-76 he held important positions in the hierarchy of the Romanian Orthodox Church in the United States. A former Securitate head, Ioan Mihai Pacepa, who defected to the West in the late 1970s, has said that Bartolomeu was sent to the United States with a "mission."
The third candidate, 56-year-old Selejan, was the only one not sullied by accusations of involvement with the secret police.
No Acknowledgment Of Collaboration
The issue of collaboration between the Securitate and the clergy has received much public attention in Romania. The late Patriarch Teoctist was criticized by many for opposing investigations into clergy members who had been accused of collaboration. After the fall of the communist regime, the church did not acknowledge the extent of the clergy's collaboration, nor did it remove tainted officials.
Alexi Kshutashvili, a Georgian theology expert living in Romania, says the issue of collaboration is a difficult one. "The Romanian media often talk about this -- that those members of the clergy who were allowed to study abroad, in Western countries, during the communist period, were in some way affiliated with the secret police, at least on the level of signing some declaration of collaboration," Kshutashvili said.
"Now to say that one was an agent of the secret police is another thing, and is difficult to say," he continued. But Kshutashvili said it is known that Ciubotea "did enjoy certain support from the political establishment, including these [latest] elections."
RFE/RL's Bucharest correspondent Sabina Fati says some people are not happy with the close ties between the church and the government even today. The church receives most of its funding from the state -- and, according to Fati, the clergy often interferes in the political process.
"The church in turn helps the state -- most blatantly during the electoral campaign, when clerics openly support one or another candidate," Fati said.
Romania's Orthodox Church has regained its popular and influential position in postcommunist Romania. Almost 87 percent of the country's population identifies with the denomination.
But Fati says that the country's clergy are not held in particularly high regard. Opinion polls show that "70 percent of believers do not really trust the priests," Fati said.
The new patriarch of the Romanian Orthodox Church will be inaugurated in three weeks.
(RFE/RL's Romanian-Moldova Service and Georgian Service contributed to this report.)