If Derek King, 13, and Alex King, 12, are convicted of first-degree murder, they would face a mandatory sentence of life in prison with no parole.
Firefighters found the body of Terry King, 40, inside his burning home. An autopsy showed King died of blunt force trauma to the head.
The two boys had disappeared, but surrendered to sheriff's officers in Pensacola two days later.
Trying boys that young as adults is unusual, but there have been two cases in Florida this year.
Nathaniel Brazill was 14 when he shot and killed his teacher in Lake Worth, Fla. He was sentenced to 28 years in prison in July after conviction for second-degree murder. He had originally been charged with first-degree murder, but the jury convicted him on the included count of second-degree murder.
In January, Lionel Tate of Pembroke Park was sentenced to life in prison for killing a 6-year-old playmate when he was 12. He said he was practicing wrestling moves he had seen on television.
The Pensacola News-Journal obtained a diary that King apparently wrote six years ago.
"The point of everything I am doing right now is to bring the family together with the exception of the mother," said the diary's final entry.
He had complained in the diary of the inattentive mother and financial problems.
James Stokes, Alex's attorney, and Sharon Potter, who represents Derek, said their first effort will be to persuade the judge to keep the boys in the Juvenile Detention Center rather than transfer them to the Escambia County Jail.
"I realize what they are charged with, but they are still only charged. We're very concerned about their safety in the adult jail," Stokes said.