Mob scion Michael Persico pleaded not guilty yesterday in Brooklyn federal court to ordering the rubout of a fellow Colombo member — the 12th and final murder in an internal family war in the early 1990s.

Persico, 54, is accused of having his henchmen whack Joseph Scopo, a mobbed-up concrete-union official, in 1993, during a war for control of the family.

He is the son of Carmine “The Snake” Persico, a gangster serving life in federal lockup.

The younger Persico was arrested last year on racketeering charges connected to debris-removal contracts at Ground Zero. He remains free on $5 million bail.

Co-defendants Francis Guerra and Theodore “Skinny Teddy” Persico, Michael’s cousin, also pleaded not guilty and were returned to their cells, where they await trial on other charges.