At a Wednesday news conference, State Attorney Jeff Siegmeister said the teens will be detained 21 days, plus an additional nine days -- one at a facility in Ocala, the other at a Gainesville detention facility -- while he makes his decision on what charges they will ultimately face and whether they will be treated as juveniles or adults.
So, what would compel the sisters to allegedly kill their older brother? Some mean treatment, they told police.
However, Columbia County Sheriff Mark Hunter told reporters that it wasn't clear what led to the shooting.
"The motive has yet to be determined," he said. "There's going to be 100,000 whys. We might not ever know why this child acted out like this."
The older girl claimed her brother had beaten her and locked her in her room. When he fell asleep, she got a gun out of her parents' room and shot him, according to a police report obtained by CNN affiliate WJAX
The unloaded gun was secured in the parents' locked bedroom, Hunter told reporters, so the 15-year-old broke an exterior window to the room, climbed in, retrieved the 9 millimeter handgun and loaded it before killing her brother with what appears to be a single gunshot.
The 11-year-old allegedly assisted her, authorities said. The 15-year-old confessed to the crime, Hunter said.
Both girls have been charged with premeditated murder and appeared in a Florida court on Wednesday. That hearing was closed to the media.
The parents, Keith and Misty Kornegay, appeared before a judge who told them they were being charged with child neglect causing great bodily harm, a second-degree felony punishable by up to 15 years in state prison.
The judge set bond at $20,000, assigned a public defender to the case and told Keith Kornegay to have no contact with the children. Misty Kornegay was told she could have contact with the kids but only with state approval and supervision.
After the hearing, Hunter told reporters, "The neglect charge has nothing to do with the immediate incident." Rather, he said, the charges stem from an incident in which the 15-year-old was locked in her room on numerous occasions with only a blanket and a bucket.
The two sisters inadvertently tipped off an officer to the Monday shooting when they left their Columbia County home and walked to the town of White Springs, nearly four miles away.
The 11-year-old called a friend's mother to tell her that she had run away. After the friend's mother arrived, she called police.
An officer came, and at first, the older girl played it cool, putting on makeup while answering some questions and dodging others, the report said.
But then she broke into tears and told the officer about her brother.
Police contacted the sheriff. That evening, deputies went to the family's home to investigate. They found the 16-year-old boy's body on the living room floor.
The children's parents were out of town on a truck driving job, but returned immediately when they received the news, Hunter said.
The three children and an additional 3-year-old daughter had been alone in the home. The toddler is now being cared for by a child protection agency.
Misty Kornegay is unemployed and would accompany her husband on some of his truck-driving trips, Hunter said, adding that leaving the 3-, 11- and 15-year-olds in the care of their 16-year-old brother is "an accepted practice."
The case is still under investigation.
While police have identified the girls, CNN is withholding their names since they are minors and have not been charged as adults.
In 2010, the Sheriff's Office visited the home on reports of vandalism and a civil matter, WJAX reported
Hunter told reporters Wednesday that police had been to the home on three previous occasions: in March 2013 for a property damage incident, in September 2013 for a "civil matter" and in July 2011 for a "juvenile issue" that turned out to be unfounded. He did not mention a 2010 incident.
Killings are uncommon in Columbia County, which is between Jacksonville and Tallahassee, Hunter said. There were no homicides there last year.