The murder of Pia Navida baffled police.

Mystery: The murder of Pia Navida baffled police.

A Sydney man who was charged with murdering a Filipino woman 19 years after the alleged crime has been acquitted after a judge found basic defects in the prosecution case.

The body of Pia Navida, 37, was found in the Royal National Park on February 1, 1992 with the contents of her handbag strewn on the ground around her.

Police determined that the one-time prostitute had been raped and then bludgeoned to death with a rock, before being her body was dragged a small distance and dumped.

But it was a further 19 years before they were able to lay charges in relation to the crime, when advances in DNA technology allowed them to match semen found inside Ms Navida's body to two men - Rodney James Paterson and Steve Isac Matthews.

Matthews pleaded guilty to rape and murder on what was meant to be the first day of the pair's murder trial last month and is now awaiting sentence.

But Mr Paterson maintained his innocence regarding both charges.

Mr Paterson's trial was told by the Crown that his DNA was found under Ms Navida's finger nails, in her anus and on her right breast.

It also heard that during interviews with police in 2009 and 2010, Mr Paterson allegedly lied to police by telling them he did not know Ms Navida, despite telling his girlfriend at the time that he thought he had had sex with her 10 times over a six-week period.

However, following the conclusion of the Crown evidence late last week, Mr Paterson's barrister asked the trial judge, Justice Geoffrey Bellew, to direct the jury to enter verdicts of not guilty to both charges on the grounds that, even at its highest, the evidence was incapable of convincing a jury that his client was guilty.

Crucially, John Stratton, SC, submitted that even if the DNA evidence proved that his client had recently had anal sex with Ms Navida, this did not prove that Mr Patterson had had any role in her rape and murder, or that he was even present when they occurred.

On Monday, Justice Bellew upheld this application, instructing the jury to acquit Mr Patterson on both charges.

"...Although that evidence is capable of placing the accused at the scene at the relevant time, it says nothing at all about his participation in the act which caused the deceased's death," Justice Bellew said in the reasons for his decision.

"Presence at the scene does not sustain an inference of participation in the killing of the deceased."

Drawing on the evidence of the forensic pathologist who undertook the autopsy of Ms Navida's body, Justice Bellew also found that there was a lack of evidence to support the Crown case that Ms Navida and Mr Paterson had been involved in a struggle shortly before her death.

"I am not satisfied that the existence of a broken rib, and the presence of the accused's DNA on the deceased's fingernails, in combination with the other matters relied upon by the Crown, sustain an inference that a struggle took place," Justice Bellew said.

"There were no injuries suggestive of forced intercourse, nor any external injury (such as bruising)."

He also found that Mr Paterson's lies to police did not amount to consciousness of guilt.

"Whilst it may be that he answered questions put by the police because he did not wish to connect himself with the events surrounding the deceased's death that does not, without more, lead to the conclusion that his motivation for making such statements was a realisation of guilt of either of the offences with which he has been charged," Justice Bellew said.

"Indeed, there were statements made by the accused, both in the course of his second interview with the police and in the two conversations with his partner, which were at odds with such a realisation."

Following his honour's direction, the jury acquitted Mr Paterson.

Steve Isac Matthews will be sentenced later this year.