Toddler Khandalyce Pearce was killed not long after the death of her mother Karlie Pearce-Stevenson, whose body was dumped in the Belanglo State Forest in 2008, police believe.
Daniel James Holdom, 41, has appeared in court charged with the murder of Ms Pearce-Stevenson.
Holdom was charged overnight with killing Ms Pearce-Stevenson almost two years before her bones were found in the forest south of Sydney.
It is understood police were able to trace Holdom's mobile phone as being in the Belanglo State Forest at the time Ms Pearce-Stevenson was killed.
NSW Homicide Squad commander Detective Superintendent Mick Willing said police believed Khandalyce was killed after her mother.
"But we are trying to establish the exact timing," he told reporters on Thursday.
No charges have been laid over Khandalyce's death.
Police will allege Ms Pearce-Stevenson was murdered between December 14 and 15, 2008.
"She sustained certain injuries to her body but I can't go further into those injuries as investigations are ongoing," Superintendent Willing said.
It is understood that, while the mother and daughter both suffered violent deaths, their injuries were different,
Police have not revealed how Holdom and Ms Pearce-Stevenson knew each other.
However, it is understood Holdom had ties in the ACT. Ms Pearce-Stevenson was last seen in Charnwood, an outer suburb of Canberra, in 2008.
Holdom appeared via audio visual link from Cessnock Correctional Centre, wearing prison greens, on Thursday morning.
His Legal Aid solicitor, Peter Cleaves, told magistrate John Chicken that his client did not wish to appear in court in any form - not even by video link.
But Mr Chicken refused the request.
"Given the nature of the charge I think it's appropriate that he appear by AVL," he said.
"It's not like he is being brought in and paraded."
Holdom was formally refused bail, although Mr Cleaves did not apply for it on his behalf.
The matter was adjourned to Sydney's Central Local Court, where Holdom has been ordered to appear via audio visual link, on November 12.
Daniel James Holdom has appeared in court charged with the murder of Karlie Pearce-Stevenson. Bail was formally refused. The case has been adjourned to Central Local Court in Sydney on November 12.
Man charged with alleged murder of Karlie Pearce-Stevenson will appear by audio visual link, despite asking not to appear before the court.
Police say Karlie Pearce-Stevenson was killed between December 14 and 15, 2008.
Police addressed the media at a press conference in Sydney today.
Media are yet to find out if the man charged with the alleged murder of Karlie Pearce-Stevenson will appear in person in court, or by video link.
A media scrum has formed outside Maitland Local Court awaiting the arrival of a man charged with the alleged murder of Karlie Pearce-Stevenson.
The man, a 41-year-old, was interviewed by detectives at Cessnock police station on Wednesday night.
Detectives arrested him at Cessnock Police Station about 4.15pm Wednesday October 28 and he was later charged with murder. He has been bail refused to appear at Maitland Local Court on Thursday October 29.
The arrest comes five years after Ms Pearce-Stevenson's remains were found in the Belanglo State Forrest, south of Sydney.
Her identity remained a mystery until earlier this month when police linked her DNA to that of a child's body found dumped in a suitcase on the side of a highway at Wynarka in South Australia in July this year.
Police last week made public Ms Pearce-Stevenson's identity and the fact that the child in the suitcase was her daughter, Khandalyce.
Detectives have said they believe the pair were killed at different times and at different locations in December 2008.
Police suspect people involved in the murder of mother and daughter also hijacked the pair's identities after killing them and raked in about $90,000 across multiple states and territories.
Earlier this month South Australian Police released dashboard camera vision of the Karoonda Highway, near Wynarka, where the faded suitcase was found.