The special allegation makes Gardner eligible for the death penalty.
Gardner is due back in court Tuesday. A preliminary hearing is scheduled for March 18. He continues to be held without bail. He was being held in solitary confinement.
The second charge, the assault with intent to rape, is connected to an incident in Rancho Bernardo Park in December. A female jogger was attacked but managed to fight off her assailant. That jogger has not been identified.
Gardner pleaded guilty and was convicted 10 years ago of molesting a 13-year-old girl. He served five years of a six-year sentence for that crime. He was on parole until 2008.
Investigators uncovered a body Tuesday believed to be Chelsea King, a missing 17-year-old teen from the San Diego area.
King, a popular straight-A student at Poway High School, disappeared while on a jog in San Diego-area Rancho Bernardo Park Thursday.
Tuesday, searchers found a body in a shallow grave at the edge of Lake Hodges in Rancho Bernardo Park, about a half-mile from where King's car was found.
The body was discovered in a heavily wooded area not observable from hillside homes or from the park. A shoe was discovered about 10 to 15 feet from the body.
The San Diego County Sheriff announced in a news conference Tuesday that authorities believed the body was Chelsea King, but positive forensic identification was not complete. King's parents were notified.
Authorities did not release evidence against Gardner, but said they do have strong physical evidence tying him to the crime.
San Diego Police Capt. Jim Collins said Tuesday that Gardner is believed to have assaulted a 22-year-old Colorado woman on a run at Rancho Bernardo Community Park in December. She was able to fight off her attacker, who was never caught. Gardner's second charge Wednesday is in connection to this incident.
In February 2009, 14-year-old Amber DuBois disappeared on her way to Escondido High School, not far from Rancho Bernardo. Authorities are investigating possible connections to that case. Maurice DuBois, Amber's father, was present at a Wednesday news conference update on Gardner's arraignment. DuBois briefly answered questions from reporters.
Tuesday night, an emotional vigil that drew thousands of mourners. There were tears, hugs and a heartfelt thank you from King's father.
"One of the nicknames I always called my daughter was, 'My Angel,'" said Brent King, Chelsea's father. "She'll always be my angel."
With silent reverence for the moment, a stream of people filed by, each holding a candle, each with special thoughts about King.
"We're here to remember a person that's part of our community and somebody that was going to have a bright future that was so brutally taken away from them for no reason," said Laura Vonnyssen, a Poway resident.
Like most people at the vigil, Vonnyssen was not a close friend of King's. In fact, she competed against her at a track meet.
"She's someone who touched everybody's lives, even if they didn't know her," Vonnyssen said.
The police were called to Gardner's parents' home for a report of vandalism. Someone had painted "Chelsea's blood is on you move out" in red on the garage door.