Police have named the man as Borce Ristevski, Karen's husband.
Mr Ristevski has been charged with one count of murder and is scheduled to appear before Melbourne's Magistrate's Court this morning.
The 47-year-old mother went missing from her home in Oakley Drive, Victoria, on the morning of June 29, 2016.
Mrs Ristevski's body was discovered on February 20 after extensive police searches.
Detectives said earlier this year Mr Ristevski is a suspect in his wife's death. He has always vehemently denied any involvement.
The couple share one daughter - Sarah, 22 - who has been spending much of her time in Asia since her mothers death last year.
At the time Mrs Ristevski went missing, The Herald Sun reported the couple fought over money before her disappearance.
This is a developing story.