It happened at 3202 Mermaid Avenue just before 9:00 Sunday night.
Investigators said the suspect was in the store earlier in the day and wanted to buy something.
He didn't have enough money and the clerk wouldn't let him buy it with what he had.
Police said the man was upset and left, but then came back with the gun.
He fired the two shots into the ceiling to scare the clerk, yelled a bunch and then left. The worker was not injured.
The second man seen in the video in the beige jacket did not steal anything. He was using the ATM and pulled his card out of the machine before leaving the store. He's not a suspect.
The suspect is described as an Hispanic man in his 30s, approx. 5'10" tall, 210lbs, wearing a black jacket, black pants and black sneakers.
Anyone with information in regards to this incident is asked to call Crime stoppers at 1-800-577-TIPS (8477). You can also submit their tips by logging onto the Crime stoppers website at www.nypdcrimestoppers.com or by texting tips to 274637 (CRIMES) then enter TIP577.