The shooting happened just before 3 p.m. on the 170th Street southbound subway station platform in the Grand Concourse section.
NYPD officials say first responding officers found a 41-year-old man shot in the thigh and groin.
The victim was taken to Lincoln Hospital where he was pronounced dead.
Officials say the victim was known by police to hang around the subway system.
They say the shooting appeared to stem from a dispute.
Officials say a suspect, also known to police, fled out of the station, wearing a blue jacket with a cream hoodie. Police are searching a nearby building.
No arrests have been made.
Officials say this is the first shooting and homicide in the subway system this year. There were three shootings in the subway last year.
B and D trains are bypassing 170 Street in both directions while the NYPD conducts an investigation at the station.
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