The defendant is charged with the arson of 66B Wesley St and the murders of David Ian Clarke (49) and Anastasia Margaret Neve (35).
Police confirmed a week after the incident that the circumstances were considered suspicious.
"Police are now treating the deaths as a double homicide and evidence suggests that they died before the fire started," a statement released at the time said.
Police refused to reveal details concerning the pair's cause of death because it was "significant" and could become key evidence that goes before a court.
Days after the initial arrest was made, police offered "identity protection" for anyone who came forward with information.
It remains unconfirmed whether that offer had been taken up.
The man charged was known to the couple, police confirmed.
The defendant remained in custody and his next appearance will in the High Court at Dunedin on June.
The Wesley St address where the fire took place was again ablaze in the early hours of this morning.
A Fire and Emergency New Zealand spokesman said they were called the house at 1.15am.
Three crews, from Lookout Point, Central Dunedin and St Kilda, were called to the fire and arrived to find it well ablaze.
Extra resources were called and firefighters remained there for most of the morning.
A fire investigator had been called to look into the cause, but the fire was yet to be declared suspicious.
A police spokeswoman said the Dunedin criminal investigation branch was investigating and would be conducting a scene examination this morning.
