The incident occurred just after 11 p.m. at the recently opened Essex Convenience Smoke Shop at 118 E. 116th Street.
Police say a 34-year-old store clerk was shot in the groin while trying to stop the gunman.
A 22-year-old customer was pistol-whipped.
Both victims were taken to Harlem Hospital, where they are listed in stable condition with non-life-threatening injuries.
It's unclear how much money was taken.
Authorities are now looking for two male suspects, one who was wearing a blue ski mask, and the other wearing a black hat with white logo.
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