A fugitive murder suspect was arrested by the FBI in the Bronx tonight on charges of killing a potential witness to drug slaying in Philadelphia, authorities said.

Jose Aldea, 22, of Philly, was charged with the execution-style murder of deli clerk Rosemary Fernandez-Rivera, 33, Monday in the Pennsylvania city.

Cops questioned the clerk a week before her death to see if she could identify suspects in the turf shooting of Louis Chevere, 22, at the deli two months ago.

Law enforcement sources believe Aldea is the masked thug who marched past other deli employees Monday night and killed the potential witness.

He was found hiding in the bathroom of a Mount Eden apartment last night and charged in the cashier’s death.

He has a lengthy rap sheet for drugs and violence, law enforcement sources said.