The discovery came only three days after sex offender John Albert Gardner III was charged with the high-profile murder of another area teen, Chelsea King, who was raped Feb. 25 as she jogged in a park near her home.
Dubois disappeared on the morning of Feb. 13, 2009, only about 100 yards from Escondido High School. In the wake of the King murder, Dubois's case received new attention and tips which led to the discovery 20 miles north of Escondido, north of the Pala Indian Reservation.
"The discovery was made in the early morning hours Saturday in a very rugged and remote area of Pala," Escondido Police Chief Jim Maher told reporters at a brief press conference Sunday afternoon. "Escondido police and sheriff's homicide detectives were following a lead in the case when they made the discovery."
He said the body was identified Saturday afternoon through dental records, and detectives notified Dubois's parents Saturday evening.
It was not immediately clear to what extent Gardner is considered a suspect in Amber's murder. Maher did not mention Gardner at the press conference, nor did he take reporters' questions.
"Any details, no matter how slight, would be inappropriate to reveal at this time," Maher said.
Dubois was featured along with other missing teens in the PEOPLE cover story "Vanished Without a Trace."