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The man is due to appear in Dunedin District Court tomorrow on one count of arson and two counts of murder.
The bodies of Anastasia Margaret Neve (35) and David Ian Clarke (49) were found inside a Wesley St property on January 22, after it was set alight.
The man was known to the couple.
Detective Inspector Steve Wood said police formally laid the murder charges earlier today at the Otago Corrections Facility.
“This is a significant milestone in the investigation, however, the dedicated CIB team still has a lot of detail to work through in order to ensure a robust, fair, and thorough investigation."
“We know the arrest for murder will assist concerned members of the community, and help the families and friends of the victims feel safer as they recover from their ordeal.”
“The families of David Clark and Anastasia Neve are aware of the arrest, and say they are relieved and thankful," Det Insp Wood said.
Police said last week they received more information on the homicide.
The week before that investigators in the double homicide promised "identity protection" for anyone who came forward with further information, in a bid to boost their collection of evidence.
A police spokeswoman said more people had come forward offering information after last the request for information.
None had requested protection of their identities.