A range of biological macromolecules as antibodies, enzymes or receptors function on principles based on selective recognition. These biological macromolecules are very often used in many technical applications due to their well-defined selectivity features. Unfortunately using of biomolecules is limited by their high production costs and low stability. Therefore, an idea of creation of synthetic materials with tailor-made molecular selectivity was presented. These materials are called molecularly imprinted polymers (MIPs). MIPs use molecular imprinting of chosen molecule to creating selective binding sites in cross-linked polymer. Technique of molecular imprinting has become one of the most efficient methods that are used for preparation of selective recognition materials. MIPs are stable, robust and have low production costs. In this work, the novel sensitive method for Staphylococcus aureus isolation and detection based on molecular imprinting was investigated. Molecularly imprinted layer was created on a surface of magnetic particles (MPs) due to ability of MPs pre-concentrate bacteria from large sample volumes. Fluorescence microscopy was used for detection of isolated bacteria.