And while the occasion marked the end of the search for the teenager, the investigation now focuses on a man accused of killing yet another teenage girl.
Amber's photo was draped on the outside of Escondido High School Monday night.
"I still see a lot of kids walking by themselves. It scares me every day I see it. We have to make changes and we're going to hopefully, with the support of other parents, change some of the laws to make all of these faces safe," said Carrie McGonicle, Amber's mother, at the vigil.
As hundreds gathered in prayer, Amber's parents spoke lovingly of their daughter, who went missing in February of last year. Her remains were discovered over the weekend. Her father spoke of his daughter's love for wolves.
"We as parents and a community need to make a change for the protection of our children and learn from the wolves that Amber so loved that as a community, we need to do it together," said Amber's father Maurice Dubois.
The tragedy has touched the entire community, as evidenced by the turnout at the vigil. Hundreds of residents, most of whom had never met the young girl, came to the candlelight vigil.
"I thank those for gathering like we have tonight. It shows such tremendous support. It helps the family," said Escondido Police Chief Jim Maher.
Escondido police are looking for answers in the Dubois' murder. Her skeletal remains were found about 10 miles from Rancho Bernardo Park, where the body of 17-year-old Chelsea King was discovered a week ago. Police are looking into any connection between their murders.
Dubois disappeared while she was walking to school on Feb. 13, 2009. Searchers found her skeletal remains Saturday near the Pala Indian Reservation. Dental records confirmed it was Dubois.
"The discovery was made early and in a very remote and rugged area of Pala, which is in northern San Diego County," said Maher.
Amber was last seen walking with a man about 200 yards from Escondido High School. She never appeared on school surveillance cameras. Unlike the search for King, there was no physical evidence recovered in the search for Dubois. The recovery of her remains a year after her disappearance came in response to a tip. But so far police aren't revealing the source of that tip.
Police want to know if Amber's death could be linked to the killing of Chelsea King. King's accused killer, 30-year-old John Albert Gardner, is in custody. He pleaded not guilty to murdering King and attempting to rape her. He is also charged with raping another woman in December in the same park where King disappeared.
Amber's parents met briefly with reporters as police announced the discovery of their daughter's remains.
"We'd like to thank everybody involved in the search, especially our huge volunteer corps. That's about all we have to say. Thank you," said Amber's father.
King's parents issued a statement saying they have spoken to Amber's family. And they share their "indescribable grief." They are consoling each other.
"My opinion is 'serial killer,'" said Blythe Kieffer, a friend of the Dubois family. "We have been suffering in this county and also in San Diego."
After news that Amber's remains were found, administrators at her high school Monday brought in extra counselors to work with the students as necessary.
"It's been hard. I've had to run out of quite a few classrooms bawling my eyes out," said Hailey Kosinski, a friend of Amber's for more than three years. "It just keeps coming and going. Something I'll never be able to forget it as long as I live. I could always go to her if I was having a bad day and I'd end up laughing with her, about whatever, she'd always find a way to cheer you up."