Richard Lyons, 42, was charged with first-degree murder Tuesday, according to the Cook County state's attorney.
In an unrelated case, police said Lyons, who is a radiology technician at Northwestern Memorial Hospital, has also been charged with aggravated criminal sexual abuse of a 15-year-old boy. That crime took place in June of 2010, authorities said.
The body of Lyons' daughter, Mya, was found near his home in the 8400-block of South Gilbert Court two and a half years ago.
"I'm confident that whomever did this, that the light will be shined on them and that person will be flushed out," Lyons said in 2008, a week after his daughter's murder.
At the time, Mya was living with her mom in suburban Addison but had come to visit her father in his Auburn-Gresham home.
Mya was stabbed to death. Her body was found in a then heavily wooded alley just a few doors from her father's home.
Within two weeks, police began to focus on Richard Lyons. He cooperated in the early days of their investigation, but then refused to talk. Soon, Lyons would become their prime suspect.
"You're supposed to be her father. You're supposed to love and care for her. You don't want to believe that," said Ericka Barnes, Mya's mother.
On Tuesday, Lt. Brandan Deenihan of the Chicago Police Department said "scientific evidence" led to charges against Lyons. But police also said that no one piece of evidence provoked the charges.
"Make no mistake, this was never a cold case...a lot of evidence to look through. It just took a while to put it together," said Supt. Jody Weis, CPD.
In the weeks that followed the Mya's murder, her mother, grandfather and other relatives said they began to get suspicious of Mya's father. For more than two years, they quietly talked with detectives who have now confirmed their worst fears.
"We always suspected he had something to do with it," said Orlando Barnes, Mya's grandfather.
Mya's grandfather said Richard Lyons drew the family's suspicion.
"I seen a person that was acting. If I had any words to say to Richard it would be 'take off that mask, you have been exposed,'" said Orlando Barnes.
Lyons' attorney said he doesn't believe there is any new evidence.
"He's maintained his innocence from day one and he's continues to maintain his innocence, and he is innocent. And if you want to go based on evidence instead of emotional cries of innocence, the fact is there's no evidence that I'm aware of," said Alan Blumenthal, Richard Lyons' attorney.
Mya's mother said she has just one question for Lyons.
"I just want to know why? What led him to do something like this?" said Ericka Barnes.