The case involved about 100 defendants, most of whom the court acquitted on Thursday. More than 40 people were convicted, 15 of them as accessories to the killings.

Fifty-eight people are believed to have died in the massacre, but the body of one of them — Reynaldo Momay, a journalist — was never found, and the defendants were found not guilty of killing him. His daughter, Maria Reynafe Castillo, said she had expected that.

“The main perpetrators got life without parole,” she said. “I am happy with that.”

Not all of the suspects have been accounted for. Eighty remain at large and are believed to be hiding in the south and likely still working with the clan, officials say. The national police have said they believe that those not in custody might be hiding in areas controlled by armed Muslim militants.

The suspects who are still at large remain a continued source of worry. Earlier this month, a man who had testified for the prosecution, Basit Taguigaya, was killed in an ambush.

“He was supposed to join me in Manila for the promulgation of the Maguindanao massacre case,” Mr. Mangudadatu told reporters recently. “No one has yet been arrested. Are the lives of those who testified also in danger?”

Three other witnesses who testified against the Ampatuan clan have also been killed as the case has wound its way through the notoriously slow Philippine criminal justice system. Andal Ampatuan Sr., who was among the accused, died of natural causes in prison.