The victims were inside Mama's Fried Chicken on Frederick Douglass Boulevard when the gunman burst in at about 8:40 p.m.
The shooting was captured on surveillance cameras both inside and outside the restaurant.
The video shows the gunman walk past the restaurant, notice the two, and then enter and open fire.
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The 13-year-old was shot in the head and taken to St Luke's Hospital in critical condition.
The 16-year-old was shot in the back and taken to Harlem Hospital.
Both victims are expected to survive, authorities said.
Detectives recognized a 17-year-old who known to them and took him into custody nearby, but police say he turned out to be a relative of the victims fleeing the restaurant.
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He was spotted on surveillance and was initially thought to be involved, but once detectives talked to him and his family, he was eliminated as a suspect.
There are no arrests, and the incident remains under investigation
The victims are believed to be part of a subset of established gangs, and the shooting may be retaliation for another shooting on same block last week.
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