Daniel McDermott, 44, was charged with raping and strangling an Orange County woman in Buena Park after a DNA test matched him to samples of genetic material collected from the victim.
McDermott was charged with murder with special circumstances that could send him to prison for life without parole if he is convicted, the Orange County District Attorney's office said in a written statement.
McDermott allegedly broke into the home of 18-year-old Gehmine Chandler, raped her and then strangled her to death.
McDermott was arrested in October by Albuquerque police after the DNA test matched the evidence from the crime scene. The initial DNA test in 1988 failed to turn up a match and the investigation was shelved until cold-case investigators reopened it in 2009.
The district attorney's office said McDermott had not provided a DNA sample to detectives in 1988.