A method of operating a semiconductor memory device includes dummy-programming selected memory cells representing all the memory cells to be programmed for a programming operation. The method also includes determining as a first group of memory cells those selected memory cells having threshold voltages less than or equal to a reference threshold voltage and determining as a second group of memory cells those selected memory cells having threshold voltages greater than the reference threshold voltage. The method further includes programming the selected memory cells by applying a first bit line voltage to the memory cells of the first group, applying a second bit line voltage different from the first bit line voltage to the memory cells of the second group, and applying a same program pulse to the memory cells of the first and second groups.