Molecularly imprinted polymer (MIP) beads for proto-hypericin recognition were prepared by suspension polymerization. In order to study the impact of monomers on the MIPs properties, various monomers such as acrylic acid (AA), hydroxyethyl methacrylate (HEMA), methacrylic acid (MAA) and itaconic acid (IA) in their combinations were crosslinked with ethylene glycol dimethacrylate (EDMA) in the presence of a complex phyto-extract template derived from Hypericum perforatum L. The synthesized MIPs and corresponding non-imprinted polymers NIPs were characterized by infrared spectroscopy analysis, morphology and thermogravimetric analysis. High-performance liquid chromatography combined with UV-Visible spectroscopy, used to investigate the recognition properties of the MIPs for various naphthodianthrones, pointed out that the MIP IA-AA system seemed to be the most adequate for favoring quantitative rebinding of proto-hypericin and proto-pseudohypericin against competitors with similar structures, like hypericin and pseudo-hypericin, which are usually present in high quantities in the primary Hypericum perforatum L. phyto-extracts.