A memory system and a method of operating the same are provided. The method includes reading least significant bit (LSB) data of a first physical page based on a first pre-read voltage and performing a most significant bit (MSB) program based on the LSB data of the first physical page when the MSB program is performed on the first physical page, defining a management area by comparing the number of error bits included in MSB data of the first physical page with a first threshold value, preforming an LSB program on a second physical page of the management area, reading LSB data of the second physical page based on a second pre-read voltage, which is lower than the first pre-read voltage, and performing the MSB program on the second physical page based on the LSB data of the second physical page.