Merrell, the toddler's mother, is now charged with aggravated child abuse and three counts of child neglect.
The couple called deputies earlier that day to report the 3-year-old missing.
They said the child was last seen playing in their backyard.
As they continued to talk to her, the mother-of-three eventually confessed that Hagwell had kicked Adelynn in the head and locked her in a closet, then carried the child's lifeless body to the woods.
Destinee Merrell, 23, told police that her boyfriend, Cory M. Hagwell, 29, kicked the child in the head because she had climbed out of her auto seat, Fox News reported. Neighbors found the children after they escaped by breaking a window. Hagwell is charged with aggravated child abuse.
The Okaloosa County Sheriff's Office added a charge of first degree murder to prior charges involving Cory Hagwell, 29, and a charge of accessory after the fact to murder for the child's mother, Destinee Merrell, 23.
The mother was charged because she took part in locking her daughter in the closet, police said.
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An autopsy determined that Adelynn died from a skull fracture to the back of the head caused by blunt-force trauma.
Both Hagwell and Merrell were arrested. It wasn't clear Saturday if Merrell or Hagwell had hired lawyers.
Merrell described hearing thuds and the sounds of the three-year-old crying 15-16 times over the past month.
Investigators further determined Merrell had left Adelynn and another child alone, locked in a room, September 1.
He was taken to the Emerald Coast Children's Advocacy Center Friday for a wellness exam and was found to be weighing less than 33 pounds (14 kilograms), a sheriff's office report cited by the newspaper said.
Authorities said that a 5-year-old boy in Merrell's care was also found to be suffering malnutrition and had "bones in all regions of his body exposed".