The use of molecular imprinted polymers (MIPs), which provides a means for preparing stationary phases with predetermined selectivity for a target molecule in capillary electrochromatography (CEC), is attractive because it combines selectivity, higher separation efficiency and shorter analysis time. A bisphenol A (BPA)-imprinted monolithic capillary BPA/PMAPA column was synthesized for the selective separation of bisphenol A (BPA) from aqueous solutions containing the competitor molecule phenol (PH), which is similar in size and shape to the template molecule. BPA-imprinted monolithic column was prepared in the presence of the template molecule, BPA, which results in the formation of recognition cavities complementary to the template molecule, after the removal of template molecule. An amino acid based monomer, N-methacryloyl-L-phenyl alanine (MAPA), was used as the functional monomer. The new stationary phase contains both charged and hydrophobic groups originating from MAPA monomer, which behaves as both an electroosmotic flow (EOF) supplier and a hydrophobic matrix. The MAPA containing BPA imprinted column behaves as a mixed mode stationary phase, as ion exchanger and hydrophobic matrix depending on the pH of the medium. Scanning electron microscopy was used to identify the structural features of the molecular imprinted column. MIP column performance was evaluated by the electrochromatographic separation of alkylbenzenes. The novelty of this work originated from dual separation mechanism shown by MAPA, which has the ability to form both hydrophobic and electrostatic interactions by the charged and hydrophobic groups of phenylalanine amino acid. This new column with mixed-mode characteristics was then used successfully as the stationary phase in CEC for the selective separation of BPA in MIP systems.