A man has gone on trial 12 years after a woman was raped at knifepoint, after a DNA match was found.

Wayne David Batchelor, 42, denies charges of rape, sexual violation, threatening to cause grievous bodily harm and unlawful possession of an offensive weapon, a knife.

Prosecutor Deirdre Elsmore said in the Christchurch District Court that the charges were brought nine years after the rape on April 1, 2000, when a DNA sample from Batchelor was found to match the profile of the offender from samples taken after the rape.

The attack occurred about 6.15am on a Saturday, when the 22-year-old woman was walking to work.

A man walked towards her in St Albans, blocked her way, pulled out a knife and said: "Do as I say, bitch. If you don't, I'll cut your throat."

He made her go down a driveway, where he raped her while he held the knife to her throat. She feared for her life.

When the offender ran off, the woman went to a nearby phonebox and rang the police, who attended quickly. A dog tracked the man over a fence and into the grounds of a church, where the track was lost.

The woman described the height of the attacker, and his build, his hair colour, eye colour and his "rounded, stubby nose".

DNA samples were taken straight away from the woman's body and underwear.

A test carried out on skin and sperm samples found on the woman, by scientists for the defence, showed DNA profiles from as many as five males, including Batchelor and the boyfriend.

"This was unexpected," Elsmore said.

"The Crown says there is only one explanation that makes sense and that is contamination."

She understood the defence would say the test brought into question all the other samples.

It would say that the science was misleading and police had arrested the wrong man because the DNA profile had been wrongly identified, she said.

Defence counsel Lee-Lee Heah said there was no doubt the woman was subjected to a horrific rape, but the police had got the wrong man.

Batchelor had maintained his innocence from the start.

She told the jury that DNA evidence was "not rock solid".

The trial before Judge Gary MacAskill is expected to last five days.

- © Fairfax NZ News