Suffolk District Attorney Daniel Conley said he authorized a murder charge for Michael McCarthy, 35, and the girl's mother, Rachelle Bond, 40, is under arrest for accessory to murder after the fact.
"At just shy of three years old, Bella Bond was a true innocent," Conley said at a news conference announcing the charges. "This child, whose very name means beauty, was murdered," he said.
The girl was known as Baby Doe as investigators launched a massive social media campaign to find out who she was and how she died.
Police immediately appealed to the public for help. Using photos of her remains, the National Center for Missing and Exploited Children created a composite image of what the girl might have looked like when she was alive.
Photos of Bella posted on her mother's Facebook page made it clear that she looked strikingly similar to the composite image.
Conley said McCarthy was being treated at a Boston hospital for a medical condition unrelated to the case. Both Bond and McCarthy are due to be arraigned on the charges Monday.
Officials from the state's child protection agency said they had contact with Bella twice, for four months in 2012 and three months in 2013. In both cases, officials described the involvement as "support for neglect," and the cases were later closed.
Rhonda Mann, a spokeswoman for the Executive Office of Health and Human Services, said the agency has been working with law enforcement to help police identify the girl.
"Now that we know her name, the story is no less tragic. DCF has not had an open case with this family for over two years, but did have brief involvement with Baby Bella as an infant," she said in a statement.
The girl's body was found June 25 inside a trash bag on Deer Island in Winthrop by a woman walking a dog.
Despite the widespread publicity, a text tip line and billboards with the girl's image, investigators were frustrated for months as they tried to learn her identity. They got their big break after Boston police received a tip and a search warrant was executed Thursday at Rachelle Bond's apartment.
Conley would not say specifically how her body got to Deer Island, but implied that her mother placed her there. He said evidence investigators uncovered led them to charge her with being an accessory after the fact to murder.
Bond had a history of drug and prostitution arrests. In 2006, she was arrested after a car she was a passenger in was stopped for a traffic violation. When Bond got out of the car, police noticed she was sitting on a syringe. She was charged with possession of a hypodermic syringe.
In 2008, she was charged in a sting operation with offering to perform sexual acts for a fee on a male police officer posing as a john.
On Rachelle Bond's Facebook page, she appears to be a doting mother, posting numerous photos of her daughter, who she calls "Bell" and "monkey."
In a posting on Aug. 18, 2014, Bond wrote: "My Bella loved her birthday party and all the awesome things she got. Broke the bank on it but it's all worth it to see her happy and laughing and smiling. Love it."
A few weeks later, on Sept. 15, 2014, a photo shows Bella wearing a tight-fitting, one-piece romper. "Look at my Bell," Bond wrote. "The outfit isn't supposed to be a catsuit ... Love her to death. I am on top of the world because of her. My life is complete again and worth living. I give her the world and more if I can..."
Conley would not comment on how the girl died, but said more information may be released when McCarthy and Bond are arraigned. There were no obvious signs of trauma to her body.
Police chased down tips from around the world, but experts determined pollen on the girl's blanket and leggings and in her hair came from trees found in New England.
Conley did not comment on a possible motive.
After three months, the washed up toddler found dead on a Boston Harbor beach and known simply as Baby Doe has been identified as Bella Bond - and her mother is in custody thanks to tip-offs from neighbors.
The tragic girl has been named as two-year-old Bella Neveah Amoroso Bond, the daughter of 40-year-old Rachelle Bond of the Boston neighborhood Mattapan.
The mother and her boyfriend, 35-year-old Michael McCarthy, have been arrested in connection with the Bella's death. McCarthy is not the girl's biological father, a law enforcement source said.
McCarthy faces a murder charge while Bond faces a charge of accessory after the fact of murder. They are expected to be arraigned on Monday.
Suffolk County District Attorney Daniel Conley said during a later briefing that information on the cause of death will be released on Monday, adding that her life ended 'by violence in the place she should have felt safest: in her home'.
'We have a very good idea of what happened to her based on evidence,' Conley said on Friday.
'We have powerful evidence has provided us a manner of death that we will be able to prove in court.'
Conley said a descriptive account of what happened to Bella would be released in a press conference on Monday.
The state medical examiner still has to confirm Bella's identity through positive DNA testing.
'The men and women who investigated this case have given her her name back. Now we will give her justice,' Massachusetts State Police Col Richard McKeon said.
DeLeo said Bond and McCarthy, who are in custody, are blaming each other for Bella's death. He also added that McCarthy has drug issues.
Oh, my God, I can't believe it,' Tamera Bond added. 'I thought the picture looked like Bella, but Bella was a little chubbier.'
Tamera Bond said the last time she saw Bella was nine months ago, in January.
Bella's grandmother, who did not want to be identified, told WCVB that she didn't know her granddaughter existed - she hadn't spoke to her daughter Bond in 14 years.
'I think we maybe have to see our priest or something because i don't know what to do. This is shocking,' she said. 'I think it's our responsibility to do something.'
A tip-off from neighbors brought the nearly three-month long search to determine the girl's identity to an end on Thursday.
The Boston Herald reported that Siomy Torres, who had lived in the Maxwell Street building on the Dorchester-Mattapan line since June 2014, said state police showed up at her home and started questioning her about her neighbor's daughter.
'They told me they were looking for the little girl, and asked me if I'd seen her,' Torres said.
She said state police showed her the composite picture of Baby Doe and she recognized it.
'I haven't seen her in months. I usually hear her because her room is against the backside of my apartment. I usually hear her crying or running around the house and I haven't heard that,' Torres said. 'I used to see her every day. Running around.'
A DCF spokeswoman said it had contact with Bella twice between August and December 2012 and June and September 2013 on allegations of neglect, WCVB reported.
'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,' DCF spokeswoman Rhonda Mann said.
'Now that we know her name, the story is no less tragic. DCF has not had an open case with this family for over two years, but did have brief involvement with Baby Bella as an infant.
'Our thoughts are with Bella's extended family as the investigation into her death continues.'
It was earlier reported on Friday that police were searching for Bond and McCarthy as persons of interest in the case.
Authorities said they were able to match Bella's identity with the clothes she was found wearing when her body was found on Deer Island in Winthrop on June 25, according to the Daily Beast.
She was wrapped in a zebra-print blanket and was wearing black-and-white polka-dot leggings.
In photos seen on social media, Bella is wearing a pair of black-and-white polka-dot leggings, but Conley would not confirm if these were the leggings she was found in.
Her body did not have fingerprints when she was found due to erosion by the tide and investigators have not determined a cause of death.
On Facebook, Bond posted several photos of Bella as they cuddled, cooked together and the mother once called Bella 'My love, my soul, my life. My heart beats because she's in my world.'
In another post she wrote: 'Love her to death. I am on top of the world because of her. My life is complete again and worth living. I give her the world and more if I can...'
On August 6, 2014, Bond made a post on her daughter's second birthday saying 'My lil bell. It's her b'day today. Happy birthday my sweetest thing ever...'
The last photos Bond shared of Bella on Facebook were on Christmas day last year.
