Her name was Bella, a child whose very name means beauty, Suffolk County District Attorney Daniel Conley said Friday.
For 85 days -- since her remains were found, wrapped in a trash bag on a rocky shoreline in Boston Harbor -- the young girl had been known only as "Baby Doe."
Rachelle Bond, 40, her mother, has been charged as an accessory after the fact in her death, Conley told reporters.
The mother's boyfriend, Michael McCarthy, 35, has been charged with murder, according to Conley. McCarthy is not Bella's biological father, according to a law enforcement source.
They will be arraigned on Monday.
"This child, whose very name means beauty, was murdered," Conley said.
Bella Amoroso Bond, just shy of 3 years old, was a "true innocent" whose short life ended "not by illness or accident but, we believe, by an act of violence in the very place where she should have felt safest -- in her home," said the Massachusetts prosecutor, declining to comment on the motive or manner of death.
The case of the mysterious girl, whose adorable brown eyes and cherubic face -- as rendered by forensic artist Christi Andrews and distributed by authorities -- caught the attention of millions after the discovery in late June of the body.
The couple was picked up after Boston homicide detectives received a tip Thursday, officials said.
McCarthy is in custody at a Boston-area hospital under treatment for a medical condition, and Bond is being held at a separate location, according to the law enforcement source.
The arrests came after a search warrant was executed in Boston's Mattapan neighborhood, officials said.
There is a case history with the girl
The state Department of Children and Families was briefly involved with Bella as an infant, but have not had a case with the girl's family in more than two years, according to department spokeswoman Rhonda Mann.
"Since June, the Department has been working closely with law enforcement on exploring dozens of leads in hopes to identify the little girl found on Deer Island," Mann said in a statement. "Now that we know her name, the story is no less tragic ... Our thoughts are with Bella's extended family as the investigation into her death continues."
Between 2001 and 2006, child welfare authorities terminated Bond's parental rights over two other children, an agency official said. One child remains in the custody of the maternal grandmother; the other was adopted by an unrelated family, according to the official.
The official said the agency provided services for Bella in August and December of 2012 and again in June and September of 2013 following neglect complaints regarding the child.
Yessiomara Torres, Bond's next-door neighbor, said the girl's mother told her she had lost custody of two other children and worried about losing custody of Bella, CNN affiliate WHDH reported.
"She said she didn't want anybody taking her away from her, that she is trying her best to be the best parent that she can be," Torres told the station.
But Torres said she hadn't heard or seen Bella since earlier this year, believing she was in state custody.
"I used to hear the little girl either crying, running around, playing," she said. "I haven't heard that for months now."
The neighbor told WHDH that Bella strongly resembled the composite authorities released after the body was found.
"It looked exactly like her," she told the station. "It's shocking and sad. She's so young... I feel sorry for that little girl. She should have been in better hands."
Remains were found in bag along shore
The tiny remains were found June 25 wrapped in a black trash bag, wearing polka dot pants lying next to a zebra blanket along the shore of Deer Island, a narrow peninsula just east of Boston's Logan Airport. Police released photos of the blanket and the polka-dot leggings she was wearing.
Authorities previously said they believe that "Baby Doe" was about 4 years old at the time of her death. She was 3 feet 6 inches tall and weighed about 30 pounds.
The National Center for Missing & Exploited Children released the composite of Baby Doe in July. Massachusetts State Police posted it on Facebook and distributed it via Twitter.
More than 50 million people saw or shared the composite.
It's unclear how long she had been dead but there was some decomposition when her remains were removed from the trash bag.
Authorities analyzed pollen found on the girl's pants and blanket and determined that it "came from trees and plants around Boston," Jake Wark, a spokesman for the Suffolk County District Attorney's Office, said last month.
"This pollen analysis also suggests that 'Baby Doe' may have been placed on the shoreline, rather than washed ashore from a great distance," Wark said.