Ben Smart and Olivia Hope vanished on New Year's morning 1998. Scott Watson was convicted of their murders.

A new appeal has been lodged on behalf of convicted killer Scott Watson with fresh evidence challenging the "two hair theory" that helped seal his conviction.

A Royal Prerogative of Mercy (RPOM) application was filed on Watson's behalf earlier this month to Governor-General Dame Patsy Reddy.

Watson is serving a life sentence after being convicted in 1999 of killing Ben Smart, 21, and Olivia Hope, 17, after they went missing from a New Year's Eve party in the Marlborough Sounds.

JOHN KIRK-ANDERSON/STUFF Scott Watson has always denied meeting the pair, let alone killing them.

He has always denied ever meeting the pair, let alone killing them. The only physical evidence linking the couple to Watson were two blonde hairs – believed to be Hope's – found on-board his home-built sloop following their disappearance.

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The evidence has long been considered to be the smoking-gun in the Crown's largely circumstantial case.

Two hairs believed to be Hope's were introduced as evidence in Watson's High Court trial. The validity of those hairs is being called into question in his latest appeal

The new appeal includes a report by forensic scientist Sean Doyle which calls into question whether the hairs were really Hope's, and criticises the way the evidence was handled.

Watson's father, Chris Watson, said he and his son had read the forensic report and fully backed the appeal.

"Scott is optimistic, hopeful, with a touch of pessimism about the whole thing," he said. "He is getting on with life, he has got a lot to get along with."

STUFF Scott Watson leaving Blenheim District Court, in 1998 following his arrest.

The appeal was brought about by Auckland man Brian McDonald, who met with Scott Watson earlier this year after researching the case. He helped raise the money to pay for the in-depth forensic report to be completed and compiled information from other researchers.

"The new evidence focuses on the how the hair samples were mishandled and how the evidence can't be looked at in isolation," McDonald said.

McDonald hoped the new evidence would persuade the government to order a retrial, or quash Watson's conviction.

The 22-page report by Doyle concluded there were significant "weaknesses" in the way ESR handled and identified the hairs which were found on a blanket aboard Watson's boat.

"The hair and DNA evidence falls some way short of current standards and, in some respects, fell short of standards at the time," Doyle said. "If adduced today, the reliability of that evidence would be strongly challenged."

Also included in the appeal is research by justice campaigner Mike Kalaugher focusing on the infamous ketch that witnesses described Hope and Smart boarding, but has never been found.

Watson, along with his father, previously filed a RPOM in 2009 which was rejected by the Governor-General on the advice of then Justice Minister Judith Collins.

A Ministry of Justice spokeswoman said officials were currently liaising with Government House on whether the latest RPOM application was in order, before being referred to the Minister of Justice for formal advice. "If and when the application is referred to the Minister of Justice by the Governor-General, normal practice is for the Minister to send the application to Ministry officials for investigation and report. At that point, the Ministry would assess what steps were necessary to address the issues in the application and begin consideration of the application."

Justice Minister Andrew Little said the fresh application had not yet been brought to his attention, but he understood the case. "In the end, I have to make the ultimate recommendation. I am well aware of the case, I know there have been a number of books and documentaries about it.

"It is one of those cases the criminal justice system gets now and then. It is very controversial, there are differing views and different interpretations of the evidence."

Gerald Hope, Olivia's father, declined to comment on the most recent development.

Watson has previously launched unsuccessful appeals to the Court of Appeal and the Privy Council, claiming his innocence. He will next be considered for parole in 2020.