BUENOS AIRES, Argentina — The elevation Wednesday of Argentine Cardinal Jorge Bergoglio as the Roman Catholic Church’s 266th pope and the first from Latin America brought cheers across South America but also served as a reminder of the church’s role during the region’s dark days of dictatorship in the latter half of the 20th century.

Born in Buenos Aires in 1936, Bergoglio, 76, was 40 when Argentina’s military overthrew the government of Isabel Peron and instigated what became known as the “Dirty War,” during which as many as 30,000 people, most of them accused of being leftists, “disappeared.” Like many priests his age, he has been accused of not doing enough to protest the carnage.

In 2005, Argentine author Horacio Verbitzsky, whose books have detailed what he said was the church’s involvement in the Dirty War, accused Bergoglio of failing to protect two fellow Jesuits who’d opposed the military junta. The two Jesuits vanished and were presumed to have been killed by security forces. Bergoglio was never charged in subsequent years, nor has any hard evidence emerged of his involvement. But the charge has lingered largely because of Verbitzsky’s prominence in Argentina.

More recently, Bergoglio has been known for his confrontations with Argentina’s last two presidents, the husband and wife team of Nestor and Cristina Kirchner.

"He was always very kind to the poor and the drug addicts, I hope he can keep those qualities in the Vatican," said Roberto D’Abbraccio Varela, 63, a Buenos Aires security guard and Roman Catholic. “There are some doubts with him about what he did during the military dictatorship but you can never know the truth and since he was never judged we have to presume he’s innocent."

Nestor Kirchner, who died in 2010, famously accused then-Cardinal Bergoglio of being “the true leader of the opposition.” During Argentina’s financial meltdown in 2001 and 2002, Bergoglio was a constant voice for the poor. He later famously lamented the rising poverty in Buenos Aires, noting that residents there “take better care of a dog than a brother.”

Bergoglio also was cool to Kirchner’s efforts to annul amnesty laws that protected those accused of crimes during the Dirty War. Among the first people to be tried after the laws were abolished was a Catholic police chaplain. Christian von Wernich was convicted and sentenced in 2007 by a federal court for participating in a series of crimes it said were “akin to genocide.” At the time of the trial, Bergoglio headed Argentina’s Conference of Bishops.

A common theme during the trial was the church’s inaction. One witness during the trial, the Rev. Ruben Capitanio, told the courtroom, “I say this with pain. Until the church recognizes its errors, we will be an unfaithful church.”

He closed his testimony by telling family members of the victims that “I apologize for still not being the church that we must be, on the side of the crucified and not the crucifiers.”

In a cable to Washington dated Oct. 11, 2007, Tony Wayne, then the U.S. ambassador to Argentina, noted the heavy political content of the case and the possible impact on Cardinal Bergoglio’s ability to oppose Kirchner’s policies.

“Many on the political left allege the church was complicit with atrocities committed by the state and believe the church has failed to account or atone for its actions,” the cable said. “The church has not yet disciplined nor defrocked Von Wernich but has sought to distance itself from the unauthorized, maverick operations of rogue priests. Nonetheless, at a time when some observers consider Roman Catholic primate Cardinal Bergoglio to be a leader of the opposition to the Kirchner administration . . . the Von Wernich case could also have the effect, some believe, of undermining the church’s (and, by extension, Cardinal Bergoglio’s) moral authority.”

In an earlier cable, dated May 10, 2007, the embassy noted that Bergoglio had actively opposed Kirchner initiatives despite having said “that the church would not get involved in politics.”

“The government appears irritated at the cardinal’s apparent preference for the opposition in this electoral year,” the cable said.

Relations with Cristina Fernandez de Kirchner, who succeeded her husband, remain tense, largely over Fernandez’s championing of same-sex marriage, which Bergoglio vehemently opposes.

Still, there was an outpouring of enthusiasm for Bergoglio’s elevation to the papacy as Pope Francis.

In Brazil, the secretary general of that country’s Conference of Bishops praised the choice, extolling Bergoglio’s commitment to fighting poverty and social injustice.

“It’s a great surprise, and a pleasant surprise,” Leonardo Steiner, head of Brazil’s Conference of Bishops, told O Globo, Rio de Janeiro’s largest daily newspaper.

Steiner said he expected Pope Francis to come to Rio in July for a global youth conference. “We are neighbors despite our disputes in soccer,” he joked.

In Peru’s capital of Lima, the comment thread on El Comercio’s lead papal story was abuzz with the prospects of a Latin American pope.

“Excellent news, it was time for a Latin American pope,” wrote Vladimir Estrada.

As might be expected, many Argentines were ecstatic. Many felt his experience battling the Kirchners would suit him well as he tackles a Vatican bureaucracy noted for its intransigence.

“He has experience fighting against people in power here, so hopefully he can use that experience to shake things up in the Vatican,” said Virginia Camon, 37, a secretary, who described herself as church-going but a believer that the church is behind the times on issues such as gay marriage.

“I’ve always admired the way Bergoglio has spoken up for the poor,” she said.

Raul Guzman, 47, who earns his living by picking up discarded cardboard on the street and recycling it, shared her hope. “I never go to church, but maybe an Argentine can help clean up the church,” he said. “The Vatican is the most corrupt place in the world.”

Emilce Cuda, the first laywoman in Argentina to receive a Vatican-recognized doctorate in theology from the Catholic University of Argentina, said Bergoglio’s election was a sign to Latin American poor that the church was with them.

“It is a sign of the times . . . that for the first time it is not a European pope, it’s a Jesuit and an American, even if a Latin American,” she said.

Bergoglio signed off on Cuda’s doctorate in 2010. She said she understood how he could be both loved and disliked.

“He is a person with a certain charisma and a certain peace when you talk to him. . . . when you saw him on the (Vatican) balcony, he didn’t seem nervous,” she said. “He is a person here in Argentina who has people for him and against him.”

Tim Johnson in Mexico City contributed. Politi and Sreeharsha are McClatchy special correspondents. Politi reported from Buenos Aires, Sreeharsha from Sao Paulo, Brazil, and Hall from Washington.