A method of operating a memory controller in a memory system including a nonvolatile memory device includes; erasing memory cells of a target memory block of the non-volatile memory device on a block basis, and then searching for a bad memory cell by a performing an erase verifying operation, comparing a threshold voltage of the bad memory cell to a reference voltage to generate comparison results, and designating as a bad area one of the entire target memory block, and a sub-block of the target memory block in response to the comparison results.