Encoding programming data based on data store in to-be-programmed unit

A method of programming data in a nonvolatile memory device comprises receiving program data to be programmed in selected memory cells of the nonvolatile memory device, reading data from the selected memory cells, encoding the program data using at least one encoding scheme selected from among multiple encoding schemes according to a comparison of the program data and the read data, generating flag data including encoding information, and programming the encoded program data and the flag data in the selected memory cells.