Geralyn Graham, 59, has been a suspect since the state's social service agency discovered Rilya was missing in March 2002, but there was never enough evidence to charge her.
But prosecutors said Graham, who has been in jail on child abuse and kidnapping charges, was implicated by a jailhouse informant, The Miami Herald reported Thursday.
Miami-Dade County State Attorney Katherine Fernandez Rundle said Graham made self-incriminating remarks heard by the informant.
The comments contained information that "only someone with knowledge of the crime possessed," the state attorney said.
The indictment said Rilya, who was 4 at the time of her death in 2000, died from "smothering and/or suffocating and/or beating."
Detectives said the unidentified informant first called authorities in August and after that had numerous conservations about the little girl's death.
Rilya's body has never been found.
2014: The Year in Music [PHOTOS]