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A 36-year-old Chadstone woman was arrested on Thursday night in Seaford, while a 35-year-old Seaford man was arrested Friday afternoon in Carrum Downs.
The pair were interviewed by police and subsequently charged with one count each of murder, police said early on Saturday morning.
Police said it was believed the incident occurred at a property on Binalong Avenue in Chadstone, where there was a suspicious fire on July 18.
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A significant search for the man, aged in his 40s, was undertaken as part of the investigation.
The body of a man, who is yet to be formally identified, was found on Railway Parade in Chadstone yesterday.
Police said it was believed the parties involved were known to each other and the investigation remains ongoing.