Ronald Washington and Karl Jordan Jr. have both been charged with "murder while engaged in narcotics trafficking and fire-arm related murder," Fox News has learned.
Additionally, Jordan Jr. has been charged "with several additional narcotics distribution counts."
Jordan Jr. was arraigned on Monday and entered a "not guilty" plea to all charges. Washington will be arraigned later this week.
Washington had reportedly been living on a couch at the home of Jam Master Jay, whose real name was Jason William Mizell, in the days before his death and was named a witness or possible suspect as far back as 2007.
Washington is currently serving time in prison for a handful of robberies he committed while running from police after the musician's death.
In court papers filed at the time, prosecutors alleged that Washington brandished a handgun in Jay's recording studio, demanding those present to the ground while another man killed the musician on Oct. 30, 2002.
Prosecutors claimed that Washington “provided cover for his associate to shoot and kill Jason Mizell."
Jay was shot once in the head by a masked man in his studio in the Queens neighborhood where he grew up. He was survived by his wife and three children.
Washington was also linked to the 1995 fatal shooting of the late Tupac Shakur's associate, Randy Walker, prior to his time sleeping on Jay's couch.
The Associated Press contributed to this report