The hearing will determine whether he must stand trial for the murder of his pregnant wife, Laci Peterson.
On Wednesday, both sides disputed the type of DNA test that prosecutors say proves a hair found in his boat was Laci Peterson's.
The hair, found in a pair of pliers on the boat Scott Peterson took fishing the day his wife disappeared, matched a genetic sample from Laci Peterson's mother, an FBI expert testified Wednesday, the first day of the preliminary hearing.
For much of the day inside a packed courtroom, FBI lab supervisor Constance Fisher testified about the controversial method of DNA analysis she specializes in that can show a genetic match between a mother and child.
She testified that a one-inch strand of hair found on pliers in the boat did not match Scott Peterson, but did match a swab of DNA taken from the mouth of his mother-in-law, Sharon Rocha.
Defense lawyer Mark Geragos is challenging the admissibility of the testimony, saying the analysis was the subject of a "raging debate" in the scientific community and suggesting that the hair sample may have been contaminated or tampered with by law enforcement.
The technique has not been widely accepted in courts, and it was only ruled admissible once in a California state court, in the case of an accused murderer in San Diego.
With the exception of a brief mention of Laci Peterson's family at the start of the hearing, the 27-year-old substitute teacher's name was never uttered again during the daylong hearing in Stanislaus County Superior Court.
The hearing is expected to last into next week, after which Judge Al Girolami will decide if Peterson is tried on two counts of murder that could lead to the death penalty.
While the proceedings are expected to reveal the broadest and most detailed look at the case police built against the 31-year-old former fertilizer salesman, the opening day turned into what a prosecutor called "DNA 101."
After Fisher wraps up her testimony, Geragos can present his own expert to dispute the science and try to get the judge to eliminate it from the hearing and prevent it from being used at trial.
Prosecutors said they planned to call the Petersons' housekeeper and Laci Peterson's family members after the expert testimony.
Fisher's testimony cast light on a key possible piece of evidence in the case, linking Laci Peterson to the boat Scott Peterson said he took fishing when his wife vanished on Christmas Eve.
The case gained national attention and led hundreds of volunteers to search up and down California. The remains of mother and fetus were found four months later in April, along San Francisco Bay, within miles of where Peterson said he had been fishing.
Peterson has been held without bail since he was arrested not far from the Mexico border with his hair bleached and $10,000 in cash. In the months after Laci Peterson's disappearance, it was disclosed that her husband was having an affair.
Geragos has said he would not only prove Peterson innocent, but would find the "real killers." The defense team has intimated that a satanic cult may have been responsible.