A two-zone SMB/chromatography hybrid system was studied to separate L-phenylalanine, which is the intermediate retained component, from a ternary amino acid mixture; glycine, L-phenylalanine, and L-tryptophane. PVP (poly-4-vinylpyridine) and deionized water were used as solid and liquid phases, respectively. Single component linear isotherms and mass transfer rates were obtained from multiple frontal tests. For the mass transfer rate, the Lapidus and Amundson linear dispersion model was used with an effective dispersion coefficient calculated from the mass transfer rate and the axial dispersion coefficient. This model was validated by comparing the frontal data with the simulation results from Aspen Chromatography 2004. A single objective genetic algorithm was employed to determine optimal operating condition. Experiments using the two-zone SMB/chromatography system were conducted to purify L-phenylalanine. The results show that the two-zone system successfully removed 95.0% of glycine and 79.2% of L-tryptophane from the ternary mixture producing a L-phenylalanine product purity of 88.2%.