The 46-year-old Dunedin man was earlier this month granted interim name suppression and remanded in custody by consent.
That followed the deaths of David Ian Clarke (49) and Anastasia Neve (35).
The pair were found dead after an early morning fire.
The police later said evidence suggested they died before the fire started.
The man who has been charged was known to the couple.
Police said he would appear in the Dunedin District Court today on one count of arson and two counts of murder.
Officers formally laid the murder charges yesterday at the Otago Corrections Facility.
Detective Inspector Steve Wood described the charge as ``a significant milestone in the investigation''.
However, the CIB team still had 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.''
He said the families of Mr Clark and Ms Neve were aware of the arrest and were ``relieved and thankful''.
Det Insp Wood urged anyone with information that might assist the investigation to contact Dunedin Police on (03) 417-4800 or Crimestoppers anonymously on 0800-555-111.
