The remains were removed from a shallow grave on the shoreline as hundreds of volunteers combed the forest and brush in Rancho Bernardo Community Park in search of the Poway High School student, whose classmates hung missing posters around campus and posted prayers to a Help Find Chelsea King Facebook page with 77,000 fans.
"This was our worst fear, that we would find her as we did today," San Diego County Sheriff Bill Gore told reporters.
A convicted sex offender was arrested Sunday and scheduled for arraignment Wednesday on charges of murder and rape.
John Albert Gardner III, 30, spent five years in prison after he was convicted 10 years ago of molesting a 13-year-old neighbor girl in his mother's townhouse, which is in the same community as the park. Gardner is also being looked at in the case of Amber Dubois, 15, who disappeared Feb. 13, 2009, while walking to Escondido High School and has still not been found.