A Harlem man has been charged in the killing of former New York City drug lord Alberto “Alpo” Martinez — a self-proclaimed “rat” who was in witness protection when he was shot dead last fall.

Shakeem Parker, 27, was already being held at Rikers Island for a prior gun case when he was indicted this month on murder and criminal possession of a weapon charges in the Oct. 31, 2021 slaying.

Martinez, 55, was behind the wheel of his red 2017 Dodge Ram, hanging out with Halloween partygoers near the Legend’s Lounge in Harlem at around 3:20 a.m. when several gunshots smashed through the window.

Prosecutors allege Parker came into the city from The Bronx early that morning and met up with his brother at a deli near 147th Street and 7th Avenue before walking over to Martinez’s truck and firing into the driver’s side window.

He then allegedly took a few steps back and squeezed off two more shots in the direction of the vehicle.

Despite being wounded, Martinez drove off, ultimately crashing into a car and stopping at around 147th Street. He was rushed to Harlem Hospital but could not be saved.

Surveillance footage caught Parker coming into Manhattan and then going back to The Bronx in a cab at around 4 a.m., after he allegedly fled the crime scene through the Harlem River Houses, prosecutors said.

Martinez — who was portrayed by rapper Cam’ron in the 2002 movie “Paid In Full” — had been hiding out in a federal witness protection program in the town of Lewiston, Maine, apparently under the name Abraham Rodriguez.

It’s unclear why he decided to come back to his old stomping grounds, and while authorities haven’t provided a motive for the slaying, police sources have said Martinez would have been in danger as soon as he returned.

The notorious drug kingpin wasn’t exactly tight-lipped about the fact that he’d betrayed former associates.

He talked openly about being a government witness in a 2020 YouTube video, saying “I’m not promoting being a rat … I’m promoting you get locked up you do what you gotta do,” The Post previously reported.

Parker, of West 149th Street, was busted on Nov. 6, 2021 for gun possession and police recovered a cellphone from him that allowed them to corroborate his movements on the night of the murder, prosecutors said.

There were also several images of Martinez and the crime scene that had already been released to the public saved on the phone, Assistant District Attorney Jung Park said during Parker’s arraignment Friday in Manhattan Supreme Court.

Parker was charged with criminal possession of a weapon again on Feb. 16 and ordered held on $500,000 cash bail in that case.

Judge Curtis Farber remanded Parker into custody after his arraignment on the indictment. His next court date in the case is March 28.