Washington: The man charged with the murder of Boston's "Baby Doe" allegedly said the girl was a "demon anyway" and that "it was her time to die", a prosecutor said in a Massachusetts court on Monday.

Michael McCarthy, 35, is being held without bond over Bella Bond's death. The girl's 40-year-old mother, Rachelle Bond, was charged as an accessory after the fact to murder and is being held on $US1 million ($1.4 million) bond. They both entered not guilty pleas.

Michael Patrick McCarthy is arraigned in the Dorchester District Court on Monday on murder charges in the death of Bella Bond. Photo: Boston Globe/AP

For months, police appealed to the public for help in identifying Baby Doe, the young girl whose body was discovered by a jogger on a Deer Island beach in June. A composite image of what the girl may have looked like went viral on social media, and her bright face was plastered on billboards throughout New England.

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Authorities on Friday finally identified Baby Doe as 2½-year-old Bella and announced charges against Ms Bond and her boyfriend, Mr McCarthy.

Mr McCarthy's attorney, Jonathan Shapiro, did not ask for his client's release on bail, the Boston Globe reported. Ms Bond's lawyer, Janice Bassil, requested a $US250 bail amount and house arrest for her client, according to the Associated Press, which said that Ms Bassil's request "drew murmurs and snickers from people in the courtroom".

Rachelle Dee Bond is arraigned on charges of acting after the fact in helping to dispose of the body of her daughter. Photo: Boston Globe/AP

Suffolk Assistant District Attorney David Deakin said on Monday that Ms Bond told investigators her daughter was being unruly one night in late May and refused to go to sleep. Mr McCarthy said he would try to calm her down; Ms Bond went to check on the two after not hearing noise for some time, Mr Deakin said.

Ms Bond then found Mr McCarthy standing over Bella "with his hand near her abdomen", Mr Deakin said. "When Ms Bond looked at Bella, her head appeared to be swollen and her face grey." Ms Bond told police that "she knew at that moment her daughter was dead", according to Mr Deakin.

"She asked Mr McCarthy what he had done and he did not tell her, but he said, 'She was a demon anyway. It was her time to die,'" Mr Deakin said in the Dorchester Municipal Court.

Mystery "Baby Doe" whose body washed up on a beach in the US has been identified as Bella Bond nearly three months after the find. Photo: Supplied

Bella's mother told police she thought Mr McCarthy put Bella's body in a bag, then put the bag in the refrigerator; soon after the girl's death, the couple got high on heroin for several days, Mr Deakin said, according to the Globe. Ms Bond also told police that Mr McCarthy eventually put Bella's body in a duffel bag and tried to dispose of it in Boston Harbour, Mr Deakin said.

The AP reported that as Mr Deakin described the investigators' findings in court, Bella's godmother, Megan Fewtrell, yelled out to Ms Bond: "I hope you rot in hell!"

Ms Fewtrell was then escorted from the courtroom, the AP reported, clutching a yellow stuffed duck that she said that Bella had taken to bed with her every night.

The news agency said that Joe Amoroso, who identified himself as Bella's father, yelled at Mr McCarthy as he was being led away: "Mike McCarthy, you're done. You won't last a day."

Police received the crucial tip last week that led to the arrests after a "lifelong" friend of Mr McCarthy's congratulated Ms Bond for recently quitting drugs and told her she could now get her daughter back, according to prosecutors. Ms Bond then "broke down" and said Mr McCarthy had killed Bella, Mr Deakin said.

Since the child's body was found on June 25, her identity and cause of death had been a mystery to investigators. She was found in a rubbish bag by a woman walking a dog on Deer Island. But there were no signs of physical trauma, and toxicology tests showed no poisons or pathogens.

Unidentified, the child came to be known publicly as Baby Doe. Computer-generated images of a chubby-cheeked girl appeared on billboards across the state and led to hundreds of tips, but none of them solved the case until last week.

"We hoped against hope that her death was not a crime," the Suffolk County district attorney, Daniel F. Conley, said. "But this child, whose very name means beauty, was murdered."

Washington Post, New York Times