Officers were called to a La Trobe Street apartment on the evening of 27 December after a 31-year-old Chinese woman was found dead.
They found the body of a 51-year-old Docklands woman in an apartment on Waterside Place.
Detectives were yet to determine the exact circumstances of the death, but were treating it as suspicious and believed it was linked to the death of the first woman, police said on Saturday.
Police urged anyone who witnessed suspicious activity around the Docklands apartment or who had CCTV between 27-29 December to come forward.
The Huntingdale man was on Friday remanded in custody to appear at the Melbourne magistrates court in May.
