The New York Daily News said Gotti was charged with ordering the fatal shootings of George Grosso in December 1988 and Bruce Gotterup in November 1991.
Gotti has been jailed since August 2008, but his three previous court appearances on racketeering charges ended with hung juries and mistrials. His father, mob figure John J. Gotti, died in prison in 2002.
"Good morning," the 45-year-old Gotti said during the first day of jury selection for his newest trial. "I am John Gotti. Here I am again."
Gotti's trial is expected to include testimony from an alleged former Mafia associate, John Alite, and disgraced New York Police Department officer Phil Baroni. The two men are expected to testify about their roles in Grosso's death.
The Daily News said Gotti will also be the focus of allegations pertaining to a March 1983 homicide in New York's Bronx borough. Specific details of that killing, which authorities suspect Gotti committed personally, were not reported.