Police say the two men got into an argument on a B12 bus on New York Avenue in Brownsville shortly before 10 a.m. and the panhandler shot the other man in the left hand.
A woman who was on the bus at the time of the shooting told NBC 4 New York the shooter had been asking passengers for money, and when the victim didn't give him cash, she says he pulled out a gun and shot him.
The suspected shooter was taken into custody and charges are pending, police say. The victim was taken to the hospital in stable condition.
It wasn't clear how many passengers were on the bus at the time.