Justin Laurens Stein, 33, is accused of killing the schoolgirl on or around January 12, 2022, at Mount Wilson, in the Blue Mountains west of Sydney.
He has pleaded not guilty.
Stein was in a relationship with Kallista Mutten at the time of the alleged murder, the Crown said. (Bianca De Marchi/AAP PHOTOS)
In a trial starting in the NSW Supreme Court on Monday, a jury heard Stein had previously served a jail sentence for drug-related offences and was undergoing treatment for heroin addiction.
He was also on medication for schizophrenia, the court was told.
Crown prosecutor Ken McKay SC said Stein was in a relationship with Charlise's mother, Kallista Mutten, at the time of the alleged murder.
The pair met while they were both serving jail sentences.
Ms Mutten was in prison for the crime of dangerous driving occasioning death, the court was told.
At some time prior to Charlise's death, Stein and Ms Mutten committed a break-and-enter together, during which two firearms were taken, the jury heard.
"One of them ... is of importance in the case the Crown brings on the murder charge," Mr McKay said.
Police found Charlise's body concealed in a barrel dumped on the banks of the Colo River. (Flavio Brancaleone/AAP PHOTOS)
While her mother was in custody, Charlise was being cared for by grandparents who lived in Tweed Heads, where she also attended school.
She flew to Sydney on December 21, 2021 with plans to spend Christmas and New Year's Eve with her mother and Stein.
On January 14, Ms Mutten contacted police and reported her daughter missing.
Police found Charlise's body four days later, on January 18, concealed in a barrel dumped on the banks of the Colo River.
She had suffered two gunshot wounds, one to her face and the other to her left lower back.
"The crown case will be that Stein shot Charlise Mutten," Mr McKay said.
Justice Helen Wilson informed the jury some aspects of the case could be confronting and reminded them of the importance of remaining impartial.
"This is a trial in which it is alleged a nine-year-old child was shot to death," she said.
"Some people find evidence of the death of a child particularly confronting.
"You will need to be assured that you can look at such evidence and ... maintain complete impartiality."
The trial is expected to run for six weeks.
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