Will County State's Attorney James Glasgow charged Scott Eby, 38, with first-degree murder and predatory criminal sexual assault of a child in the 2004 death of Riley Fox, who vanished from her home and whose body was later found in a creek four miles away.
Eby is doing time for raping his sister in 2005, says CBS News Correspondent Cynthia Bowers.
According to the criminal complaint, the 6-foot-2, 230-pound Eby held the bound girl under water until she drowned.
Her death gained widespread media attention, both during the search in Wilmington, Ill., where authorities say Eby lived, and after authorities accused her father, Kevin Fox.
Kevin Fox was charged after he implicated himself under intense questioning. But he later said he only did so in exchange for leniency and after losing hope during an overnight interrogation that lasted more than 14 hours.
Fox spent eight months in jail in the killing before DNA evidence gathered from the girl and from duct tape placed over her mouth showed he was not her killer. Glasgow, whose predecessor charged Fox, cleared the father after taking office.
The FBI says it was able to establish a DNA link between Eby and Fox's murder, Bowers reports.
"While nothing will bring back riley fox, we hope the events that led to (Eby being charged) will help bring some closure to the family," the FBI's Michael Kosanovich told reporters.
Fox and his wife, Melissa, were awarded $12.2 million in damages after they accused Will County investigators of fabricating evidence. A federal appeals court last month upheld Kevin Fox's claim he was falsely arrested but reduced the award to $8.6 million.
Glasgow told reporters Thursday there was no indication Fox and Eby ever knew each other, and the prosecutor stressed: "Kevin Fox is innocent in this case."
"I've never dealt with a case this heart-wrenching that took this long to get a resolution," Glasgow said, crediting the FBI with cracking the case since entering it over the past year or so.
Glasgow refused to discuss what the father told investigators during questioning that led to him being accused. But Glasgow called Fox's statements "significant" and insisted that "most prosecutors would have been hard-pressed to not file charges after viewing that videotape of Kevin Fox's statement."
Glasgow said he has four months to decide whether to seek the death penalty against Eby, who is serving seven-year prison sentences on each of two unrelated Will County convictions of criminal sexual assault.
Eby, an inmate at the medium-security Lawrence Correctional Center in Sumner, won't be eligible for parole until mid-2017, according to the Illinois Department of Corrections Web site.
Eby also has served prison time for burglary and forgery.