The encapsulation of individual nanoparticles has gained great attention as a method for both stabilizing nanoparticles and tailoring their surface properties. In particular, the encapsulation of nanoparticles with silica shells is advantageous for bioconjugation and applications to (nano)biotechnology. Herein we report a method for constructing gold nanoparticle (AuNP)/silica core/shell hybrid structures by biomimetic silicification of silicic acids. The procedure consists of surface-initiated, atom transfer radical polymerization of 2-(dimethylamino)ethyl methacrylate (DMAEMA) from AuNPs and biomimetic polycondensation of silicic acids by using poly(DMAEMA) as a synthetic counterpart for silaffins that are found in diatoms. The resulting AuNP/silica hybrids were characterized by Fourier transform infrared spectroscopy, energy dispersive x-ray spectroscopy, UV-vis spectroscopy and transmission electron microscopy. In addition, the immobilization of biological ligands onto the hybrids was investigated for potential applications to biotechnology. As a model ligand, biotin was attached onto the AuNP/silica hybrids through substitution reaction and Michael addition reaction, and the attachment was confirmed by fluorescence microscopy after complexation with fluorescein-conjugated streptavidin.