The 89-year-old was fatally beaten in October 2018 on the day he was transferred to a federal prison in West Virginia.
He died from blunt force trauma less than 12 hours after he arrived at the prison.
Three men, Fotios "Freddy" Geas (55), Paul "Pauly" J. DeCologero (48) and Sean McKinnon (36) were charged with conspiracy to commit first-degree murder on Wednesday.
The U.S. Attorney's Office for the Northern District of West Virginia announced on Thursday that Geas and DeCologero have also been charged with aiding and abetting first-degree murder, and assault resulting in serious bodily injury.
As Bulger was a former FBI informant, it is suspected that the murder was orchestrated by another inmate in retaliation.
Bulger was the leader of the Irish-American organised crime group the Winter Hill Gang from 1977 to 1995.
The notorious mobster was on the run from the US government since 1994 and in 1999 he was placed on the FBI’s most wanted list before he was caught and apprehended in California in 2011.
He went on trial in 2013 for 32 counts of racketeering, money laundering, extortion and weapons charges, including complicity in 19 murders.
Bulger was found guilty of 31 counts including 11 murders and racketeering. He was given two life sentences plus five years, which he was serving at the time of his death.
His father, James Joseph Bulger Snr. was from Canada and his mother, Jane Veronica ‘Jean' McCarthy, was a first-generation Irish immigrant.
In January, his family failed to sue the United States government in a wrongful death suit.
Bulger’s nephew, the administrator of his estate tried to sue the Bureau of Prisons and 30 unnamed members of the prison system.
The suit claimed that prison officials failed to protect the gangster by putting him in harm's way by moving him to a prison that the plaintiff claims was known for intimate violence.
US District Judge John Preston Bailey granted the government’s motion to dismiss the lawsuit.
In dismissing the suit, he said that courts have little power to intervene in prison housing decisions or to allow prisoners to sue prison officers for damages.
In his decision to dismiss the case, Judge Bailey wrote: “The federal Bureau of Prisons “must provide for the protection, safekeeping, and care of inmates, but this does not guarantee a risk-free environment.”
“Decisions about how to safeguard prisoners are generally discretionary.”