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

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

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.