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Mms6 is a small acidic protein which is tightly bound to magnetite in the bacterium Magnetospirillum magneticum AMB-1. Mms6 has been previously shown to promote ironbinding capacity as well as modulate the size and morphology of magnetic iron oxide crystals in vitro. In this study, we synthesized iron oxide crystals by using a monolayer-modified substrate. A self-assembled monolayer of octadecyltrimethoxysilane was modified on a silicon substrate. Recombinant Mms6 protein was attached to the substrate through the hydrophobic interactions between the protein molecules and the monolayer. The immobilization of protein molecules on the substrate surface was confirmed by fluorescent labeling of these molecules and subsequent fluorescence microscopy. This protein-modified substrate was then used as a template for iron oxide crystal formation in a ferrous solution. Scanning electron microscopy revealed sitespecific formation of iron oxide crystals in substrate regions with immobilized proteins. This use of proteins might provide an alternative method for the bottom-up fabrication of nano-sized magnetic particles.