Geralyn Graham, 59, was charged with kidnapping and three counts of aggravated child abuse causing great bodily harm for actions in the months leading up to the 2001 disappearance of Rilya Wilson. Graham is already serving a prison sentence for fraud.
Her roommate, Pamela Graham, was charged with child abuse causing no great harm and child neglect.
The charges stop short of the date of Rilya's suspected disappearance, which remains unsolved.
"We would hope that Rilya Wilson is alive," Miami-Dade police director Robert Parker said. "But in actuality, we fear that actually she's not alive."
Police said that in the last five months of 2000, Geralyn Graham punished the girl by locking her in an animal cage, tying her to her bed and confining her in a laundry room. She could get a life sentence if convicted.
Pamela Graham, 39, who is cooperating with investigators, is accused of failing to protect the girl from the abuse. She could get 10 years.
The state Department of Children & Families discovered in April 2002 that Rilya was missing and that its caseworkers had not made required visits to check on her for at least 15 months.
Rilya was an infant when she was taken by the state from her homeless, crack-addicted mother.
Pamela Graham had custody of the girl and was receiving state aid as her caregiver, while Geralyn Graham claimed to be her grandmother. The women initially identified themselves as half-sisters, but Pamela Graham told co-workers that Geralyn was her wife.
The Grahams say the 4-year-old girl was taken from their home by a DCF worker in January 2001. The agency and police denied that.
"This was really a lie, and I emphasize it was a fabrication and a concoction," Parker said.
Lawyers for the two women did not immediately return calls for comment after the arrests.
Geralyn Graham was sentenced to three years behind bars last year on charges that included accepting welfare payments for the girl long after she disappeared. Pamela Graham was sentenced to two years probation.
Rilya's disappearance led to management changes and a blue-ribbon committee's investigation of DCF. "As a result of the Rilya Wilson case the department has made numerous, significant improvements to ensure this type of tragic crime cannot be repeated," DCF spokesman Bill Spann said.
Rilya's last assigned social worker, DeBorah Muskelly, was placed on probation for official misconduct and agreed to repay the state $2,736 for filing false time sheets.