One was a former member of Parliament sometimes known as “Rambo.” The other was a former top African soccer executive.

Both appeared before the International Criminal Court on Tuesday charged with war crimes and crimes against humanity, the first alleged perpetrators the court has ever tried from the long-running and ongoing conflict in the Central African Republic.

The two accused men, Patrice-Edouard Ngaïssona, the former soccer official, and Alfred Yékatom, the former legislator, were leaders of the mostly Christian militias known as the anti-balaka that have attacked Muslim civilians during the brutal civil war that has wracked the Central African Republic since 2013.

The charges they face include murder, torture, persecution, cruel treatment, mutilation, and recruiting child soldiers. Mr. Ngaïssona is also charged with rape and extermination.

“The events are shocking to the conscience and so arresting in scale that they transgress the very nature of our humanity,” the prosecutor, Kweku Vanderpuye, told the court. “The victims of the Central African Republic deserve to be seen. They deserve to be heard. And they deserve their day in court. Justice must prevail.”

Anti-balaka sometimes translates as anti-machete, and the groups that took the name were mostly Christian and animist fighters who battled mostly Muslim rebels known as the Seleka. Both groups stand accused of committing atrocities against civilians over the course of the conflict.

Although the events that the trial will examine took place eight years ago, the same civil war is still upending the lives of Central Africans, despite the presence of Russian military advisers, Rwandan troops, and United Nations peacekeepers.

In recent months, the conflict has taken a strange twist. In the lead up to a December presidential election, Muslim and Christian rebels from either side, previously sworn enemies, teamed up to disrupt the polls. They launched attacks, cut off access to the capital, Bangui, and occupied major towns. More than 200,000 people have fled their homes, on top of the 1.3 million already displaced.

Mr. Yékatom, known by many nicknames including “Rambo,” was an Army officer before the conflict. In 2013, he became a senior anti-balaka leader, allegedly commanding 3,000 people. In 2016, he was elected as a member of the country’s Parliament.

Mr. Ngaïssona has said himself that he was a political coordinator of anti-balaka militias. Later, in 2018, he became a senior official at the Confederation of African Football.

Mr. Ngaïssona was part of the inner circle of François Bozizé, a president who took power in a coup, and ruled for over a decade before he was overthrown by Seleka rebels in 2013.

The anti-balaka carried out attacks throughout the western provinces of a country that was 15 percent Muslim before the conflict, the prosecutor said. Sexual slavery and rape by anti-balaka forces has been documented by Human Rights Watch.

The trial focuses on attacks that took place from September 2013 through December 2014, part of a strategy, Mr. Vanderpuye said, to oust the Seleka and reinstall Mr. Bozizé as president.

“The objective of their strategy was to reclaim power. The means, the consequences — unfortunately that’s why we’re here,” he said, adding that Mr. Ngaïssona was “fully aware that the group, he was helping to structure, arm, finance, instruct, and organize would inevitably target the Muslim civilian population in western C.A.R. He knew the vengeance within them.”

Both men pleaded not guilty.

“I don’t recognize myself in the charges brought against me,” Mr. Ngaïssona said.

“I have understood everything, and I categorically say that these charges are not correct,” Mr. Yékatom said.

Their trial is expected to last for around two years.

Perpetrators among the Seleka are being investigated and will also face justice before the Netherlands-based court, the prosecutor said. A Seleka leader, Mahamat Said, was handed over to the I.C.C. in January.

“There’s tragedy enough to go all around,” Mr. Vanderpuye said.

The fact that Seleka and anti-balaka rebels had teamed up to disrupt December’s election showed that the conflict was not a religious one at a community level, said Anthony Fabrice Kettemalet, a human-rights activist and schoolteacher who founded Bird of Peace, an organization that promotes nonviolence in the Central African Republic. Rather, he said, politicians had used religious divides as a tool to manipulate people and gain political power.

“We’ve lived for 50 years without justice,” Mr. Kettemalet said. “We hope that it’s just the first step in a long journey.”

Efforts to try perpetrators at home are underway, too. The Central African Republic set up a Special Criminal Court in 2015, and though it has not yet held a trial, it is carrying out investigations. It is reliant on the United Nations, and does not have enough funding, however.

There has been more success in the country’s ordinary courts. A year ago, the Bangui Court of Appeal sentenced 28 militiamen for crimes including the murder of civilians and U.N. peacekeepers.

Tuesday’s proceedings were broadcast live on Central African radio and television, and via videolink in a courtroom in Bangui.

“Impunity cannot be an option,” Mr. Vanderpuye said, as around 100 victims listened in 3,400 miles away, at the administrative tribunal in Bangui. “Only the systematic conviction of these crimes and abuses will help protect the civilian population.”

Moussa Abdoulaye contributed reporting from Bangui.

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