The accused killer of Run-DMC’s Jam Master Jay has been hit with two new charges, Brooklyn federal prosecutors announced Friday.

Karl Jordan Jr., 36, has been indicted on one count each of conspiracy to distribute and possession with intent to distribute controlled substances and use of firearms in connection with a drug-trafficking crime. If convicted of the new raps, he would face a minimum of five additional years in prison.

The new charges don’t relate to the 2002 execution-styling shooting of hip-hop legend Jay, whose real name was Jason Mizell.

Jordan is accused of pumping a bullet into Mizell’s head at his Queens recording studio over a drug deal gone bad — with the alleged help of co-defendant Ronald Washington, 56.

Both men were busted in August for the infamous Oct. 30, 2002, slaying and are being held without bail.

Mizell formed the legendary hip-hop group Run-DMC with Darryl McDaniels and Joseph “Run” Simmons — the brother of Def Jam Records founder Russell Simmons.