Defence barrister Theo Kassimatis told a Supreme Court jury on Friday that Ian Thomas had arrived home to find his mother, Pauline, 63, had been strangled by his father, William, 65, who was standing there armed with a single-barrelled shotgun.

Mr Kassimatis said Ian Thomas struggled with his father for the gun before shooting him in the chest in self-defence.

He said Ian Thomas, still reeling from seeing his mother's dead body, then used a wooden pick axe handle to hit his dead father across the head.

"It's ugly but it's not murder," the defence barrister said. "That's what happened."

Mr Thomas, 38, has pleaded not guilty to murdering his parents, who had been married for 40 years and had five children, at their Great Alpine Road home between Wangaratta and Tarrawingee, on April 21, 2013.

Mr Kassimatis  said Ian Thomas' married lover, Jacinta Emselle – who claimed Mr Thomas later confessed to her that he had killed his parents –  would feature prominently during the trial and the jury would have to assess her truthfulness, credibility and reliability.

The defence barrister said Ms Emselle was a liar and she would lie again in the witness box.

Crown prosecutor Peter Rose, SC, had earlier told the jury Ian Thomas strangled his mother in a shed before lying in wait for his father to return home.

Mr Rose said Mr Thomas then confronted his father and shot him in the chest with the single-barrelled shotgun before hitting him in the head with a wooden pick axe handle.

In his opening address, Mr Rose warned the jurors he was going to play a confronting 38-minute crime scene video which showed blood and the dead couple's bodies.

The prosecutor said that while two of Mr Thomas' sisters claimed they had had a loving relationship with their parents, Mr Thomas, his brother and another sister claimed their upbringing had been troubled and their relationship with their parents had been strained.

Mr Rose said Mr Thomas, a former sailor with the Royal Australian Navy before becoming an electrician, harboured some resentment towards his parents, which was exacerbated by his problems with alcohol.

Mr Thomas had checked into a rehabilitation clinic in Queensland in 2010 to seek help for alcohol dependency, where he met Jacinta Emselle, a married mother of two living in Meredith, between Ballarat and Geelong.

Mr Rose said the pair had begun a sexual relationship, which was continuing at the time of the murders.

The prosecutor said that when Mr Thomas had been receiving counselling in September 2012 for his drinking problems, he had exhibited serious emotional issues towards his father.

On the day of the alleged murders, Mr Thomas had been in the shed removing stickers from his van when his mother came out to see him, Mr Rose said.

It was the Crown's case that Mr Thomas attacked his mother and strangled her.

The prosecutor said Mr Thomas then lay in wait for his father to return to the property armed with the single-barrelled shotgun, leaving one light on in the main house and a tap running.

Police later found the bodies wrapped in doonas.

Mr Rose said that after killing his father, Mr Thomas left the property, before calling Ms Emselle and leaving a message on her voicemail asking her to call him, saying "it's a matter of life or death".

The prosecutor told the jury Mr Thomas and Ms Emselle then met the next day at the Cremorne hotel in Geelong, where Ms Emselle claimed he had confessed to the killings.

Mr Rose said Mr Thomas tried to set up a false alibi by calling the family homestead and later dumped the shotgun and other evidence in bushland.

The trial before Justice Lex Lasry continues.