As he sat in prison awaiting trial for the murder of his brother-in-law Scott Guy, Manawatu farmer Ewen Macdonald's wife told him their marriage was over.

Macdonald - married to Mr Guy's sister, Anna - was found not guilty of the murder on July 3, after a four-week trial in the High Court at Wellington, nearly two years after Mr Guy was shot through the throat in the driveway of his Aorangi Road home, near Feilding, on July 8, 2010.

Macdonald was arrested in April last year and charged with the murder. He has been in custody ever since.

When Mrs Macdonald gave evidence at her husband's trial, media noted she was no longer wearing her wedding ring, and a just-published article in North and South magazine reveals she has a new partner.

Macdonald's parents, Kerry and Marlene, found out about the relationship in January this year - several months after it began.

Kerry, Marlene and Anna visited Macdonald in prison two days later to break the news to him.

"I told Anna, `visiting's for an hour; you go in first and then we'll go in after and pick up the pieces," Kerry Macdonald said.

Anna Macdonald left after 25 minutes, and when Macdonald's parents went to visit him, he was relatively calm.

Kerry Macdonald said it was the toughest time in the lead-up to the trial, describing it as "more s***, another day".

Both Kerry and Marlene Macdonald say they are positive their son is innocent.

Macdonald remains in custody ahead of an appearance in Palmerston North District Court on July 31 to set a sentencing date on a series of other charges he has admitted, including an arson and criminal damage to two houses on Mr Guy's property in 2008 and 2009.

Kerry Macdonald told North and South that while those acts were inexcusable, "it's a big jump from burning something down to pulling a trigger".